Improved homology dependent repair genome editing

ABSTRACT

Compounds and related reagents, systems, methods, and compositions for increasing the frequency of homology directed repair (HDR) of target genomic sites with genome editing molecules are provided.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Patent Application No. 62/876,519, filed Jul. 19, 2019, which is incorporated herein by reference in its entirety.

BACKGROUND

Homology-Directed Repair (HDR) is a genome editing method that can be used for precise replacement of a target genomic DNA site with the sequence from a provided DNA template containing the desired replacement sequence. While the results of HDR are quite desirable, it does not work well for a number of reasons. One of the biggest problems is its low overall occurrence frequency, especially when compared to the alternative non-homologous end joining (NHEJ) repair mechanism often triggered by the genome editing molecules that cleave targeted editing sites in the genome. While most cells may have several pathways that could mediate HDR, some of them are most active during the cell cycle, diminishing the success rate of HDR in typical cell culture conditions.

SUMMARY

Disclosed herein are methods, systems, eukaryotic cells (e.g., plant cells), and compositions (e.g., cell culture compositions) that can provide for increased frequencies of modification of a target editing site of the eukaryotic cell genome with a donor template polynucleotide by Homology-Directed Repair (HDR) in comparison to a control. Features of such methods, systems, eukaryotic cells (e.g., plant cells), and compositions (e.g., cell culture compositions) that can provide for such increased frequencies of HDR include provision of a composition comprising at least one HDR promoting agent selected from the group consisting of a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof in combination with genome editing molecules comprising a sequence-specific endonuclease which cleaves a target editing site in a eukaryotic cell genome and a donor template DNA molecule having homology to the target editing site.

Methods provided herein include methods for increasing Homology Directed Repair (HDR)-mediated genome modification of a plant cell genome, comprising: providing genome editing molecules to a plant cell, wherein the plant cell is exposed to an effective concentration of a composition comprising at least one HDR promoting agent selected from the group consisting of a 5-substituted 2,4-oxazolidinedione, a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; wherein the genome editing molecules comprise an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; whereby the genome editing molecules modify the plant cell genome by HDR at a frequency that is increased in comparison to a control method wherein a control plant cell is provided with the genome editing molecules but is not exposed to at least one of said HDR promoting agents or any combination thereof.

Systems provided herein include system for modification of a plant gene, comprising: a plant cell; at least one HDR promoting agent selected from the group consisting of a 5-substituted 2,4-oxazolidinedione, 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; and genome editing molecule(s) comprising: an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; wherein the plant cell is associated with, contacts, and/or contains and effective amount of the HDR promoting agent and the genome editing molecule(s).

Methods provided herein include methods for making a plant cell having a genomic modification, comprising: providing genome editing molecules to a plant cell, wherein the plant cell is exposed to an effective amount of at least one HDR promoting agent selected from the group consisting of a 5-substituted 2,4-oxazolidinedione, 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; wherein the genome editing molecules comprise an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; whereby the genome editing molecules modify the plant cell genome by homology directed repair (HDR) at a frequency that is increased in comparison to a control; and isolating or propagating a plant cell comprising the genome modification, thereby making the plant cell having a genomic modification.

DETAILED DESCRIPTION

Unless otherwise stated, nucleic acid sequences in the text of this specification are given, when read from left to right, in the 5′ to 3′ direction. Nucleic acid sequences may be provided as DNA or as RNA, as specified; disclosure of one necessarily defines the other, as well as necessarily defines the exact complements, as is known to one of ordinary skill in the art. Where a term is provided in the singular, the inventors also contemplate embodiments described by the plural of that term.

The phrase “allelic variant” as used herein refers to a polynucleotide or polypeptide sequence variant that occurs in a different strain, variety, or isolate of a given organism.

The term “and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

As used herein, the terms “Cpf1” and “Cas12a” are used interchangeably herein to refer to the same RNA-directed nuclease.

As used herein, the phrase “effective concentration,” when used to describe a concentration of an HDR promoting agent or composition comprising the HDR promoting agent, is a concentration sufficient to exert a desired outcome (e.g., increased HDR). In certain embodiments, an effective concentration is a concentration of the agent or composition which is sufficient to provide at least a 1.5-fold increase in the frequency of HDR-mediated gene editing events in comparison to a control wherein the agent or composition is absent.

As used herein, the phrase “gene-editing” includes genome modification by homology-directed repair (HDR), base editing, and non-homologous end joining (NHEJ) mechanisms. Such gene-editing includes embodiments where a sequence-specific endonuclease and a donor template DNA are provided.

As used herein, an “exogenous” agent or molecule refers to any agent or molecule from an external source that is provided to or introduced into a system, composition, a eukaryotic or plant cell culture, reaction system, or a eukaryotic or plant cell. In certain embodiments, the exogenous agent (e.g., polynucleotide, protein, or compound) from the external source can be an agent that is also found in a eukaryotic or plant cell. In certain embodiments, the exogenous agent (e.g., polynucleotide, protein, or compound) from the external source can be an agent that is heterologous to the eukaryotic or plant cell.

As used herein, a “heterologous” agent or molecule refers: (i) to any agent or molecule that is not found in a wild-type, untreated, or naturally occurring composition, eukaryotic cell, or plant cell; and/or (ii) to a polynucleotide or peptide sequence located in, e.g., a genome or a vector, in a context other than that in which the sequence occurs in nature. For example, a promoter that is operably linked to a gene other than the gene that the promoter is operably linked to in nature is a heterologous promoter.

As used herein, the terms “comprise,” “comprises,” comprising,” “include,” “includes,” and “including” can be interchanged and are to be construed as at least having the features to which they refer while not excluding any additional unspecified features.

As used herein, phrases such as “frequency of HDR,” “HDR frequency,” and the like refer to the number of HDR-mediated events at a target editing site in comparison to the total number of target editing sites analyzed. The total number of target editing sites is the sum of: (a) target editing sites having NHEJ-mediated events; (b) target editing sites having no changes; and (c) target editing sites having HDR-mediated events. HDR-mediated events include precise insertions of heterologous sequences into a target editing site that do not contain any unintended nucleotide insertions, deletions, or substitutions in either the inserted heterologous sequence, the homologous sequences that flank the heterologous insert, or in the sequences located at the junction of the heterologous sequence and the homologous sequences.

As used herein, the phrase “eukaryotic cell” refers to any cell containing a nucleus and thus includes mammalian (e.g., human, livestock, and companion animal cells), insect cells, reptile cells, plant cells (e.g., monocot and dicot plant cells), yeast cells, and fungal cells (e.g., filamentous and non-filamentous fungi).

As used herein, the phrase “plant cell” can refer either a plant cell having a plant cell wall or to a plant cell protoplast lacking a plant cell wall.

As used herein, the phrase “plant cell-compatible salt” refers to a salt of a compound that can provide for uptake of the compound by a plant cell.

The term “polynucleotide” as used herein is a nucleic acid molecule containing two (2) or more nucleotide residues. Polynucleotides are generally described as single- or double-stranded. Where a polynucleotide contains double-stranded regions formed by intra- or intermolecular hybridization, the length of each double-stranded region is conveniently described in terms of the number of base pairs. Embodiments of the systems, methods, and compositions provided herein can employ or include: (i) one or more polynucleotides of 2 to 25 residues in length, one or more polynucleotides of more than 26 residues in length, or a mixture of both. Polynucleotides can comprise single- or double-stranded RNA, single- or double-stranded DNA, double-stranded DNA/RNA hybrids, chemically modified analogues thereof, or a mixture thereof. In certain embodiments, a polynucleotide can include a combination of ribonucleotides and deoxyribonucleotides (e.g., synthetic polynucleotides consisting mainly of ribonucleotides but with one or more terminal deoxyribonucleotides or synthetic polynucleotides consisting mainly of deoxyribonucleotides but with one or more terminal dideoxyribonucleotides), or can include non-canonical nucleotides such as inosine, thiouridine, or pseudouridine. In certain embodiments, the polynucleotide includes chemically modified nucleotides (see, e.g., Verma and Eckstein (1998) Annu. Rev. Biochem., 67:99-134). Chemically modified nucleotides that can be used in the polynucleotides provided herein include: (i) phosphorothioate, phosphorodithioate, or methylphosphonate internucleotide linkage modifications of the phosphodiester backbone; (ii) nucleosides comprising modified bases and/or modified sugars; and/or (iii) detectable labels including a fluorescent moiety (e.g., fluorescein or rhodamine or a fluorescence resonance energy transfer or FRET pair of chromophore labels) or other label (e.g., biotin or an isotope). Polynucleotides provided or used herein also include modified nucleic acids, particularly modified RNAs, which are disclosed in U.S. Pat. No. 9,464,124, which is incorporated herein by reference in its entirety.

As used herein, the phrase “Reactive Oxygen Species” (ROS) refers to radical and non-radical oxygen species formed by the partial reduction of oxygen. Examples of ROS include hydrogen peroxide, a superoxide radical, a peroxide ion, a hydroperoxyl radical, and/or a hydroxyl radical.

As used herein, the phrase “target editing site” refers to a DNA sequence that contains all sequences required for recognition by a sequence-specific endonuclease. For an RNA guided sequence-specific endonuclease, the target editing site thus includes the PAM site and the adjacent sequence that is complementary to the crRNA-portion of the guide RNA.

As used herein, the phrase “target gene” can refer to either a gene located in the genome that is to be modified by gene editing molecules provided in a system, method, composition and/or eukaryotic cell provided herein. Embodiments of target genes include (protein-)coding sequence, non-coding sequence, and combinations of coding and non-coding sequences. Modifications of a target gene include nucleotide substitutions, insertions, and/or deletions in one or more elements of a gene that include a transcriptional enhancer or promoter, a 5′ or 3′ untranslated region, a mature or precursor RNA coding sequence, an intron, a splice donor and/or acceptor, a protein coding sequence, a polyadenylation site, and/or a transcriptional terminator. In certain embodiments, all copies or all alleles of a given target gene in a diploid or polyploid plant cell are modified to provide homozygosity of the modified target gene in the plant cell. In embodiments, where a desired trait is conferred by a loss-of-function mutation that is introduced into the target gene by gene editing, a plant cell, population of plant cells, plant, or seed is homozygous for a modified target gene with the loss-of-function mutation. In other embodiments, only a subset of the copies or alleles of a given target gene are modified to provide heterozygosity of the modified target gene in the plant cell. In certain embodiments where a desired trait is conferred by a dominant mutation that is introduced into the target gene by gene editing, a plant cell, population of plant cells, plant, or seed is heterozygous for a modified target gene with the dominant mutation. Traits imparted by such modifications to certain plant target genes include improved yield, resistance to insects, fungi, bacterial pathogens, and/or nematodes, herbicide tolerance, abiotic stress tolerance (e.g., drought, cold, salt, and/or heat tolerance), protein quantity and/or quality, starch quantity and/or quality, lipid quantity and/or quality, secondary metabolite quantity and/or quality, and the like, all in comparison to a control plant that lacks the modification. The plant having a genome modified by gene editing molecules provided in a system, method, composition and/or plant cell provided herein differs from a plant having a genome modified by traditional breeding (i.e., crossing of a male parent plant and a female parent plant), where unwanted and random exchange of genomic regions as well as random mitotically or meiotically generated genetic and epigenetic changes in the genome typically occurs during the cross and are then found in the progeny plants. Thus, in embodiments of the plant (or plant cell) with a modified genome, the modified genome is more than 99.9% identical to the original (unmodified) genome. In embodiments, the modified genome is devoid of random mitotically or meiotically generated genetic or epigenetic changes relative to the original (unmodified) genome. In embodiments, the modified genome includes a difference of epigenetic changes in less than 0.01% of the genome relative to the original (unmodified) genome. In embodiments, the modified genome includes: (a) a difference of DNA methylation in less than 0.01% of the genome, relative to the original (unmodified) genome; or (b) a difference of DNA methylation in less than 0.005% of the genome, relative to the original (unmodified) genome; or (c) a difference of DNA methylation in less than 0.001% of the genome, relative to the original (unmodified) genome. In embodiments, the gene of interest is located on a chromosome in the plant cell, and the modified genome includes: (a) a difference of DNA methylation in less than 0.01% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the original (unmodified) genome; or (b) a difference of DNA methylation in less than 0.005% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the original (unmodified) genome; or (c) a difference of DNA methylation in less than 0.001% of the portion of the genome that is contained within the chromosome containing the gene of interest, relative to the original (unmodified) genome. In embodiments, the modified genome has not more unintended changes in comparison to the original (unmodified) genome than 1×10A-8 mutations per base pair per replication. In certain embodiments, the modified genome has not more unintended changes than would occur at the natural mutation rate. Natural mutation rates can be determined empirically or are as described in the literature (Lynch, M., 2010; Clark et al., 2005).

To the extent to which any of the preceding definitions is inconsistent with definitions provided in any patent or non-patent reference incorporated herein by reference, any patent or non-patent reference cited herein, or in any patent or non-patent reference found elsewhere, it is understood that the preceding definition will be used herein.

HDR promoting agents that include a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof are provided herein for use in systems, methods, and compositions that provide for improved homology dependent repair (HDR) in eukaryotic cell gene editing experiments in comparison to control experiments.

TABLE 1 HDR Promoting agents Compound CAS No. Structure Description¹ SC-9 102649-78-5

Protein kinase C activator Pregnanolone 128-20-1

GABAA receptor positive allosteric modulator ML 3403 549505-65-9

p38 MAPK inhibitor Daminozide 1596-84-5

Selective KDM2/7 inhibitor Rosiglitazone 122320-73-4

Potent and selective PPAR-gamma agonist; antidiabetic agent. SB 743921 Hydrochloride 940929-33-9

Kinesin spindle protein (KSP) inhibitor Ispinesib 336113-53-2

High affinity and selective allosteric KSP inhibitor 2- Chloroadenosine 146-77-0

Adenosine receptor agonist Edaglitazone 213411-83-7

Potent and selective PPAR gamma agonist; antidiabetic IBMX 28822-58-4

PDE inhibitor (non- selective) PIM-1 Inhibitor 2 477845-12-8

Pim-1 kinase inhibitor Ro 3306 872573- 93-8

Cyclin-dependent kinase (cdk) 1 inhibitor STF 31 724741-75-7

NAMPT inhibitor; also GLUT1 inhibitor ML 228 135171-62-0

Hypoxia Inducible Factor pathway activator MI 14 715934-43-2

Potent and selective PI 4- kinase IIIbeta inhibitor ¹Activities observed in at least certain mammalian cells.

TABLE 2 5-substituted 2,4-Thiazolidinedione and 5-substituted 2,4-oxazolidinedione HDR Promoting Agents 5-substituted 2,4- thiazolidinedione

Rosiglitazone 122320-73-4

Edaglitazone 213411-83-7

Ciglitazone 74772-77-3

Lobeglitazone 607723-33-1

Pioglitazone 112529-15-4

Troglitazone 97322-87-7

Mitoglitazone 146062-49-9

Darglitazone 141200-24-0

Englitazone 109229-58-5

Netoglitazone 161600-01-7

Rivoglitazone 185428-18-6

Balaglitazone 199113-98-9

5-substituted 2,4-oxazolidinedione

5-[[4-[2-[methyl(pyridin-2- yl)amino]ethoxy]pheny]methyl]- 1,3-oxazolidine-2,4-dione

5-[[4-[2-(5-methyl-2-phenyl-1,3- oxazol-4-yl)ethoxy]-1- benzothiophen-7-yl]methyl]-1,3- oxazolidine-2,4-dione

The generic 5-substituted 2, 4-thiazolidinediones and 5-substituted 2,4-oxazolidinediones set forth in Table 2 also encompass the 5-substituted 2, 4-thiazolidinediones and 5-substituted 2,4-oxazolidinediones, and methods of synthesis described in the U.S. Pat. Nos. 6,380,191, 6,313,113, 6,172,089, 5,665,748, 5,441,971, 5,075,300, 4,997,948, 4,918,091, 4,725,610, and 4,582,839, which are each incorporated herein by reference in their entireties. The generic 5-substituted 2, 4-thiazolidinediones and 5-substituted 2,4-oxazolidinediones set forth in Table 2 also encompass 5-substituted 2, 4-thiazolidinediones and 5-substituted 2,4-oxazolidinediones described in Momose et al., 2002. The generic 5-substituted 2,4-oxazolidinediones set forth in Table 2 also encompass 5-substituted 2,4-oxazolidinediones comprising the R groups of the 5-substituted 2, 4-thiazolidinediones Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), and Balaglitazone (CAS No. 199113-98-9). Two examples of 5-substituted 2,4-oxazolidinediones comprising the R groups of the 5-substituted 2, 4-thiazolidinediones Rosiglitazone (CAS No. 122320-73-4) and Edaglitazone (CAS No. 213411-83-7) are set forth in Table 2 as 5-[[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]methyl]-1,3-oxazolidine-2,4-dione and 5-[[4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl]methyl]-1,3-oxazolidine-2,4-dione, respectively.

Bioactive analogs of the compounds of Table 1 or Table 2 include compounds wherein at least one group and/or atom in the compound of Table 1 or Table 2 is substituted with a distinct group and/or atom to provide a distinct compound with HDR promoting activity. In certain embodiments, the group and/or atom is substituted with a group and/or atom with similar polarity, valency, and/or steno characteristics. Examples of substitutions of groups in a compound of Table 1 or Table 2 which can provide for a bioactive analog include: (i) substitution of a halogen (e.g.; Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I)) for another halogen; (ii) a substitution of a C1 to C6 alkyl or C1 to C6 alkoxy group with a different C1 to C6 alkyl or C1 to C6 alkoxy group, respectively (e.g., C2 alkyl for a C3, C4, C5, or C6 alkyl; or a branched alkyl or alkoxy for an unbranched (straight-chain) alkyl or alkoxyl; or C1 alkoxy for a C2, C3, C4, C5, or C6 alkoxy); (iii) a substitution of an unsubstituted phenyl group with a substituted phenyl group, wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen; and/or, a substitution of a substituted phenyl group with a different substituted phenyl group wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen. In certain embodiments, such bioactive analogs of the compounds of Table 1 or Table 2 can be identified by assaying the analogs either alone or in parallel with a compound of Table 1 or Table 2 for the ability to modify the plant cell genome by HDR at a frequency that is increased in comparison to a control. Such controls include mock treatments of plant cells or plants with a solvent (e.g., DMSO) and genome editing molecules or with genome editing molecules alone.

In certain embodiments, the compounds of Table 1 or Table 2 are provided to plant cells as plant cell compatible salts. Plant cell compatible salts of a compound of Table 1 or Table 2 can include sodium, potassium, ammonium, hydrochloric acid (HCl), acetate, amine (e.g., monomethylamine, ethanolamine, diglycolamine, dimethyl amine, isopropylamine), or trimesium salts. In certain embodiments, salts of the aforementioned compounds can be provided to plant cells in a composition that further comprises one or more adjuvants such as a surfactant.

In certain embodiments, the compounds of Table 1 or Table 2 are provided to plant cells as esters (i.e., in an esterified form). Such esters include esters formed by esterification of a carboxylic acid group which is present in the compound set forth in Table 1 (e.g., CAS No. 1596-84-5; CAS No. 715934-43-2). Such esters include esters formed by esterification of a carboxylic acid group which has been added to a compound set forth in Table 1 or 2. Examples of suitable esters include methyl, ethyl, propyl, butyl, hexyl, heptyl, and octyl esters.

In certain embodiments, HDR is increased in isolated plant cells or plant protoplasts (i.e., are not located in undissociated or intact plant tissues, plant parts, or whole plants). In certain embodiments, the plant cells are obtained from any plant part or tissue or callus. In certain embodiments, the culture includes plant cells obtained from a plant tissue, a cultured plant tissue explant, whole plant, intact nodal bud, shoot apex or shoot apical meristem, root apex or root apical meristem, lateral meristem, intercalary meristem, seedling, whole seed, halved seed or other seed fragment, zygotic embryo, somatic embryo, immature embryo, ovule, pollen, microspore, anther, hypocotyl, cotyledon, leaf, petiole, stem, tuber, root, callus, or plant cell suspension. In certain embodiments, the plant cell is derived from the L1 or L2 layer of an immature or mature embryo of a monocot plant (e.g., maize, wheat, sorghum, or rice).

In certain embodiments of the methods, systems, and compositions provided herein, HDR promoting agent (e.g., HDR promoting agents that include a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) or composition comprising the HDR promoting agent are provided to a plant, plant part, plant tissue, or plant cell at an effective concentration that provides for increased HDR frequencies in comparison to a control plant, plant part, plant tissue, or plant cell which has not been exposed to the HDR promoting agent or composition. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant, plant part, plant tissue or plant cell to the HDR promoting agent at a concentration of least about 0.1 μM, 0.25 μM, 0.5 μM, or 1 μM to about 10 μM, 25 μM, 50 μM, 100 μM, or 500 μM. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant, plant part, plant tissue or plant cell to the HDR promoting agent at a concentration of least about 0.1 μM to about 10 μM, about 0.1 μM to about 25 μM, about 0.1 μM to about 50 μM, about 0.1 μM to about 100 μM, or about 0.1 μM to about 500 μM. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant, plant part, plant tissue or plant cell to the HDR promoting agent at a concentration of least about 0.25 μM to about 10 μM, about 0.25 μM to about 25 μM, about 0.25 μM to about 50 μM, about 0.25 μM to about 100 μM, or about 0.25 μM to about 500 μM. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant, plant part, plant tissue or plant cell to the HDR promoting agent at a concentration of least about 0.5 μM to about 10 μM, about 0.5 μM to about 25 μM, about 0.5 μM to about 50 μM, about 0.5 μM to about 100 μM, or about 0.5 μM to about 500 μM. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant, plant part, plant tissue or plant cell to the HDR promoting agent at a concentration of least about 1 μM to about 10 μM, about 1 μM to about 25 μM, about 1 μM to about 50 μM, about 1 μM to about 100 μM, or about 1 μM to about 500 μM. In certain embodiments, an effective concentration of the HDR promoting agent or composition comprising the HDR promoting agent is a concentration that provides for exposure of a plant cell to the HDR promoting agent at a concentration of least about 0.5 μM, 1 μM, 2 μM, or 4 μM to about 6 μM, 10 μM, 25 μM, or 50 μM.

In certain embodiments of the methods, systems, and compositions provided herein, HDR promoting agent (e.g., HDR promoting agents that include a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) or composition comprising the HDR promoting agent are provided can increase the frequency of HDR in comparison to a control plant cell which has not been exposed to the HDR promoting agent or composition by a factor of at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, or 7-fold. In certain embodiments, the HDR promoting agent or composition comprising the same can increase the frequency of HDR by a factor of about 1.5-fold, 2-fold or 3-fold to about 6-fold, 8-fold, or 10-fold.

In certain embodiments, HDR is increased in plant cells that are located in undissociated or intact plant tissues, plant parts, plant explants, or whole plants. In certain embodiments, the plant cell can be located in an intact nodal bud, a cultured plant tissue explant, shoot apex or shoot apical meristem, root apex or root apical meristem, lateral meristem, intercalary meristem, seedling, whole seed, halved seed or other seed fragment, zygotic embryo, somatic embryo, immature embryo, ovule, pollen, microspore, anther, hypocotyl, cotyledon, leaf, petiole, stem, tuber, root, or callus. In certain embodiments, the explants used include immature embryos. Immature embryos (e.g., immature maize embryos) include 1.8-2.2 mm embryos, 1-7 mm embryos, and 3-7 mm embryos. In certain embodiments, the aforementioned embryos are obtained from mature ear-derived seed, leaf bases, leaves from mature plants, leaf tips, immature inflorescences, tassels, immature ears, and silks. In various aspects, the plant-derived explant used for transformation includes immature embryos, 1.8-2.2 mm embryos, 1-7 mm embryos, and 3.5-7 mm embryos. In an aspect, the explants used in the disclosed methods can be derived from mature ear-derived seed, leaf bases, leaves from mature plants, leaf tips, immature inflorescences, tassel, immature ear, or silks. In certain embodiments, the plant cell is a pluripotent plant cell (e.g., a stem cell or meristem cell). In certain embodiments, the plant cell is located within the L1 or L2 layer of an immature or mature embryo of a monocot plant (e.g., maize, wheat, sorghum, or rice). In certain embodiments, methods of editing genomes of whole plants, seeds, embryos, explants, or meristematic tissue published in WO2018085693, which is incorporated herein by reference in its entirety, can be adapted for use in the plant cells and related systems, methods, compositions, or cultures provided herein.

In certain embodiments, the plant cells can comprise haploid, diploid, or polyploid plant cells or plant protoplasts, for example, those obtained from a haploid, diploid, or polyploid plant, plant part or tissue, or callus. In certain embodiments, plant cells in culture (or the regenerated plant, progeny seed, and progeny plant) are haploid or can be induced to become haploid; techniques for making and using haploid plants and plant cells are known in the art, see, e.g., methods for generating haploids in Arabidopsis thaliana by crossing of a wild-type strain to a haploid-inducing strain that expresses altered forms of the centromere-specific histone CENH3, as described by Maruthachalam and Chan in “How to make haploid Arabidopsis thaliana”, protocol available at www[dot]openwetware[dot]org/images/d/d3/Haploid_Arabidopsis_protocol[dot]pdf; (Ravi et al. (2014) Nature Communications, 5:5334, doi: 10.1038/ncomms6334). Haploids can also be obtained in a wide variety of monocot plants (e.g., maize, wheat, rice, sorghum, barley) or dicot plants (e.g., soybean, Brassica sp. including canola, cotton, tomato) by crossing a plant comprising a mutated CENH3 gene with a wildtype diploid plant to generate haploid progeny as disclosed in U.S. Pat. No. 9,215,849, which is incorporated herein by reference in its entirety. Haploid-inducing maize lines that can be used to obtain haploid maize plants and/or cells include Stock 6, MHI (Moldovian Haploid Inducer), indeterminate gametophyte (ig) mutation, KEMS, RWK, ZEM, ZMS, KMS, and well as transgenic haploid inducer lines disclosed in U.S. Pat. No. 9,677,082, which is incorporated herein by reference in its entirety. Examples of haploid cells include but are not limited to plant cells obtained from haploid plants and plant cells obtained from reproductive tissues, e.g., from flowers, developing flowers or flower buds, ovaries, ovules, megaspores, anthers, pollen, megagametophyte, and microspores. In certain embodiments where the plant cell or plant protoplast is haploid, the genetic complement can be doubled by chromosome doubling (e.g., by spontaneous chromosomal doubling by meiotic non-reduction, or by using a chromosome doubling agent such as colchicine, oryzalin, trifluralin, pronamide, nitrous oxide gas, anti-microtubule herbicides, anti-microtubule agents, and mitotic inhibitors) in the plant cell or plant protoplast to produce a doubled haploid plant cell or plant protoplast wherein the complement of genes or alleles is homozygous; yet other embodiments include regeneration of a doubled haploid plant from the doubled haploid plant cell or plant protoplast. Another embodiment is related to a hybrid plant having at least one parent plant that is a doubled haploid plant provided by this approach. Production of doubled haploid plants provides homozygosity in one generation, instead of requiring several generations of self-crossing to obtain homozygous plants. The use of doubled haploids is advantageous in any situation where there is a desire to establish genetic purity (i.e. homozygosity) in the least possible time. Doubled haploid production can be particularly advantageous in slow-growing plants, such as fruit and other trees, or for producing hybrid plants that are offspring of at least one doubled-haploid plant.

In certain embodiments where the HDR promoting agents are used to increase HDR in plant cells, as well as the related methods, systems, compositions, or reaction mixtures provided herein can include plant cells obtained from or located in any monocot or dicot plant species of interest, for example, row crop plants, fruit-producing plants and trees, vegetables, trees, and ornamental plants including ornamental flowers, shrubs, trees, groundcovers, and turf grasses. In certain non-limiting embodiments, the plant cells are obtained from or located in alfalfa (Medicago sativa), almonds (Prunus dulcis), apples (Malus x domesfica), apricots (Prunus armeniaca, P. brigantine, P. mandshurica, P. mume, P. sibirica), asparagus (Asparagus officinalis), bananas (Musa spp.), barley (Hordeum vulgare), beans (Phaseolus spp.), blueberries and cranberries (Vaccinum spp.), cacao (Theobroma cacao), canola and rapeseed or oilseed rape, (Brassica napus), carnation (Dianthus caryophyllus), carrots (Daucus carota sativus), cassava (Manihot esculentum), cherry (Prunus avium), chickpea (Cider arietinum), chicory (Cichorium intybus), chili peppers and other capsicum peppers (Capsicum annuum, C. frutescens, C. chinense, C. pubescens, C. baccatum), chrysanthemums (Chrysanthemum spp.), coconut (Cocos nucifera), coffee (Coffea spp. including Coffea arabica and Coffea canephora), cotton (Gossypium hirsutum L.), cowpea (Vigna unguiculata), cucumber (Cucumis sativus), currants and gooseberries (Ribes spp.), eggplant or aubergine (Solanum melongena), eucalyptus (Eucalyptus spp.), flax (Linum usitatissumum L.), geraniums (Pelargonium spp.), grapefruit (Citrus xparadisi), grapes (Vitus spp.) including wine grapes (Vitus vinifera), guava (Psidium guajava), hemp and cannabis (e.g., Cannabis sativa and Cannabis spp.), hops (Humulus lupulus), irises (Iris spp.), lemon (Citrus limon), lettuce (Lactuca sativa), limes (Citrus spp.), maize (Zea mays L.), mango (Mangifera indica), mangosteen (Garcinia mangostana), melon (Cucumis melo), millets (Setaria spp, Echinochloa spp, Eleusine spp, Panicum spp., Pennisetum spp.), oats (Avena sativa), oil palm (Ellis quineensis), olive (Olea europaea), onion (Allium cepa), orange (Citrus sinensis), papaya (Carica papaya), peaches and nectarines (Prunus persica), pear (Pyrus spp.), pea (Pisa sativum), peanut (Arachis hypogaea), peonies (Paeonia spp.), petunias (Petunia spp.), pineapple (Ananas comosus), plantains (Musa spp.), plum (Prunus domesfica), poinsettia (Euphorbia pulcherrima), Polish canola (Brassica rapa), poplar (Populus spp.), potato (Solanum tuberosum), pumpkin (Cucurbita pepo), rice (Oryza sativa L.), roses (Rosa spp.), rubber (Hevea brasiliensis), rye (Secale cereale), safflower (Carthamus tinctorius L), sesame seed (Sesame indium), sorghum (Sorghum bicolor), soybean (Glycine max L.), squash (Cucurbita pepo), strawberries (Fragaria spp., Fragaria x ananassa), sugar beet (Beta vulgaris), sugarcanes (Saccharum spp.), sunflower (Helianthus annus), sweet potato (Ipomoea batatas), tangerine (Citrus tangerina), tea (Camellia sinensis), tobacco (Nicotiana tabacum L.), tomato (Lycopersicon esculentum), tulips (Tuhpa spp.), turnip (Brassica rapa rapa), walnuts (Juglans spp. L.), watermelon (Citrulus lanatus), wheat (Tritium aestivum), or yams (Discorea spp.).

In certain embodiments, the eukaryotic cells (e.g., plant cells) where the HDR promoting agents are used to increase HDR can be cells that are (a) encapsulated or enclosed in or attached to a polymer (e.g., pectin, agarose, or other polysaccharide) or other support (solid or semi-solid surfaces or matrices, or particles or nanoparticles); (b) encapsulated or enclosed in or attached to a vesicle or liposome or other fluid compartment; or (c) not encapsulated or enclosed or attached. In certain embodiments, the cells can be in liquid or suspension culture, or cultured in or on semi-solid or solid media, or in a combination of liquid and solid or semi-solid media (e.g., plant cells or protoplasts cultured on solid medium with a liquid medium overlay, or plant cells or protoplasts attached to solid beads or a matrix and grown with a liquid medium). In certain embodiments, the cells encapsulated in a polymer (e.g., pectin, agarose, or other polysaccharide) or other encapsulating material, enclosed in a vesicle or liposome, suspended in a mixed-phase medium (such as an emulsion or reverse emulsion), or embedded in or attached to a matrix or other solid support (e.g., beads or microbeads, membranes, or solid surfaces).

In a related aspect, the disclosure provides arrangements of eukaryotic cells (e.g., plant cells) where the HDR promoting agents are used to improve HDR frequencies in the systems, methods, and compositions described herein, such as arrangements of cells convenient for screening purposes or for high-throughput and/or multiplex transformation or gene editing experiments. In an embodiment, the disclosure provides an arrangement of multiple cells comprising: (a) the HDR promoting agents; and optionally (b) genome editing molecules. In certain embodiments, the arrangements of cells can further comprise at least one chemical, enzymatic, or physical delivery agent. In another embodiment, the disclosure provides an array including a plurality of containers, each including at least one cell having increased HDR-mediated genome modification frequencies. In an embodiment, the disclosure provides arrangements of cells provided with the HDR promoting agents and optionally the genome editing molecules, wherein the cells are in an arrayed format, for example, in multi-well plates, encapsulated or enclosed in vesicles, liposomes, or droplets (useful, (e.g., in a microfluidics device), or attached discretely to a matrix or to discrete particles or beads; a specific embodiment is such an arrangement of multiple cells having increased HDR-mediated genome modification frequencies provided in an arrayed format, further including at least one genome editing molecules (e.g., an RNA-guided DNA nuclease, at least one guide RNA, or a ribonucleoprotein including both an RNA-guided DNA nuclease and at least one guide RNA), which may be different for at least some locations on the array or even for each location on the array, and optionally at least one chemical, enzymatic, or physical delivery agent.

In the systems and methods provided herein, eukaryotic cells (e.g., plant cells) can be exposed to one or more HDR promoting agents and/or one or more gene editing molecules in any temporal order. In certain embodiments, the HDR promoting agents and gene editing molecules are provided simultaneously. In other embodiments, the genome editing molecules are provided after the HDR promoting agents are provided. In other embodiments, the gene editing molecules are provided before the HDR promoting agents are provided. In summary, the HDR promoting agents can be provided to a eukaryotic cell (e.g., a plant cell) either previous to, concurrently with, or subsequent to exposing the cell to the gene editing molecules.

In certain embodiments of the systems, methods, and compositions provided herein, the plant cell exposed to one or more HDR promoting agents set forth in Table 1, Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, or an ester thereof, is also exposed to and/or maintained under hypoxic conditions. Normal (i.e., “normoxic”) oxygen conditions comprise about 20% oxygen by volume. Hypoxic conditions used in the systems, methods, and compositions provided herein can in certain embodiments comprise about 14%, 13%, 12%, 11%, or 10% to about 8%, 7%, 6%, or 5% oxygen by volume. In certain embodiments, hypoxic conditions can comprise treating the plant cells with a hypoxia mimetic (e.g., desferrioxamine or cobalt chloride). In certain embodiments, a hypoxic condition can comprises maintaining the cell in a liquid culture media having a dissolved oxygen concentration that is lower than the dissolved oxygen concentration obtained when the liquid culture media is under normoxic conditions. Such exposure of the plant cell to the hypoxic condition can in certain embodiments be limited to a period of time necessary to realize improvements in gene editing frequencies (e.g., prior to and/or during association, contact, and/or containment to/of an HDR promoting agent and/or gene editing molecule; prior to and/or during exposure and/or after to an HDR promoting agent and/or gene editing molecule). Such exposure and or maintenance of a plant cell under hypoxic conditions can be achieved in the context of a plant cell in isolated form (e.g., as a protoplast), a plant cell in a plant embryo, plant callus, especially embryogenic callus, in an isolated plant tissue or part (e.g., an ovule, anther, leaf, meristematic tissue, and the like), or in a whole plant. In certain embodiments, the plant cell in any of the aforementioned contexts can be in a liquid or solid culture medium that includes about 20, about 40, or about 60 to about 80, about 100, about 120, or about 150 millimolar Ca2+ and/or Mg2+, and is exposed to and/or maintained under hypoxic conditions. In certain embodiments, the plant cells (e.g., plant protoplasts) are exposed to the hypoxic conditions about 5, 10, 15, 30, or 45 minutes to about 60, 75, 90, or 120 minutes after exposure to the gene-editing molecules and/or HDR promoting agent. In certain embodiments, the combination of the aforementioned hypoxic conditions with an HDR promoting agent provides a synergistic increase in frequencies of gene editing through homology directed repair (HDR) pathways that exceeds the sum of the increases in HDR provided by the hypoxic conditions and HDR promoting agents alone. In certain embodiments, the combination of the aforementioned hypoxic conditions with an HDR promoting agent and any of the aforementioned divalent cations provides a synergistic increase in frequencies of gene editing through homology directed repair (HDR) pathways that exceeds the sum of the increases in HDR provided each of the hypoxic conditions, HDR promoting agents, and divalent cations alone. In certain embodiments of any of the aforementioned systems, methods, and compositions, the HDR promoting agent is selected from the group consisting of a 5-substituted 2,4-oxazolidinedione, a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof. In certain embodiments of any of the aforementioned systems, methods, and compositions, the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7); Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.

Embodiments of the systems, methods, or compositions provided herein include cultures wherein the plant cell exposed to one or more HDR promoting agents set forth in Table 1, Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, or an ester thereof, is also exposed to or treated with an enzymatic and/or a non-enzymatic ROS scavenging agent. In certain embodiments, such exposure or treatment with the enzymatic and/or a non-enzymatic ROS scavenging agent results in lowered concentrations of ROS (e.g., hydrogen peroxide, a superoxide radical, a peroxide ion, a hydroperoxyl radical, and/or a hydroxyl radical) in the exposed or treated plant cell in comparison to an unexposed or untreated plant cell. In certain embodiments, the non-enzymatic ROS scavenging agents include low-molecular-weight antioxidants, including lipid-soluble antioxidants and water-soluble antioxidants (e.g., low-molecular-weight thiol antioxidants, pro-thiols, ascorbic acid, tocopherols, carotenoids, flavonoids, butylated hydroxytoluene, and butylated hydroxyanisole). Suitable low molecular weight thiol compounds include compounds having a molecular weight of 1,000 daltons (Da) or less. In certain embodiments, the non-enzymatic ROS scavenging agents are provided at a concentration of about 0.1 to about 10 millimolar, or about 1, 2, or 4 to about 8 or 10 millimolar. Specific embodiments include cultures wherein the culture medium includes about 0.1 to about 10 millimolar or about 1, 2, or 4 to about 8 or 10 millimolar low-molecular-weight thiol antioxidants; see, e.g., Pivato et al. (2014) Archives Biochem. Biophys., 560:83-99. Low-molecular-weight thiol antioxidants useful in the systems, methods, and compositions include glutathione (gamma-glutamylcysteinyl glycine), cysteine, cysteinyl glycine, gamma-glutamyl cysteine, N-acetylcysteine, cysteine, thiocysteine, homocysteine, lipoic acid, and/or dithiothreitol (any of which can also be used in combination with each other at a similar final thiol concentration). ROS scavenging agents useful in the systems, methods, and compositions also include pro-thiols (e.g., L-2-oxothiazolidine-4-carboxylate (OTC)) which are converted to thiols in the cell. In certain embodiments, the plant cell is exposed or treated with enzymatic ROS scavenging agents. Enzymatic ROS scavenging agents include any catalase, ascorbate peroxidase, a dehydroascorbate reductase, guaiacol peroxidase, monodehydroascorbate reductase, a peroxidase, and/or superoxide dismutase. In certain embodiments, an enzymatic ROS scavenging agents is provided in the culture medium. In certain embodiments, an enzymatic ROS scavenging agent or polynucleotides encoding the same can be introduced into the plant cell (e.g., by transient or stable transformation, transfection, or with a delivery agent). A combination of at least one enzymatic and at least one non-enzymatic ROS scavenging agent can also be used. Specific embodiments also include plant cell or plant protoplast cultures wherein the culture medium includes about 20, about 40, or about 60 to about 80, about 100, about 120, or about 150 millimolar Ca2+, and/or in which the culture medium includes about 0.1, about 0.25, about 0.5, about 0.75, about 1, or about 2 to about 4, about 6, about 8, or about 10 millimolar low-molecular-weight thiol antioxidant. Further embodiments encompassed are plant cell or plant protoplast cultures wherein the culture medium includes combinations of divalent cations and low-molecular-weight antioxidants, with the individual components present in the culture at concentrations similar to those listed above. In certain embodiments, the plant cells (e.g., plant protoplasts) are exposed to the ROS scavenging agents about 5, 10, 15, 30, or 45 minutes to about 60, 75, 90, or 120 minutes after exposure to the gene-editing molecules and/or HDR promoting agent. In certain embodiments, the plant cells (e.g., plant protoplasts) are exposed to the ROS scavenging agents prior to or at the same time that they are exposed to the gene-editing molecules and/or HDR promoting agent. In certain embodiments, the combination of the aforementioned ROS scavenging agents with an HDR promoting agent provides a synergistic increase in frequencies of gene editing through homology directed repair (HDR) pathways that exceeds the sum of the increases in HDR provided by the ROS scavenging agents and HDR promoting agents alone. In certain embodiments, the combination of the aforementioned ROS scavenging agents with an HDR promoting agent and any of the aforementioned divalent cations provides a synergistic increase in frequencies of gene editing through homology directed repair (HDR) pathways that exceeds the sum of the increases in HDR provided by the ROS scavenging agents, HDR promoting agents, and divalent cations. In certain embodiments of any of the aforementioned systems, methods, and compositions, the HDR promoting agent is selected from the group consisting of a 5-substituted 2,4-oxazolidinedione, a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof. In certain embodiments of any of the aforementioned systems, methods, and compositions, the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.

In certain embodiments, the plant cell or plant protoplast cultures are exposed to the HDR promoting agents, a composition or culture media comprising the HDR promoting agents, or to the HDR promoting agents and aforementioned hypoxic conditions, ROS scavenging agents, and/or Ca 2+ concentrations immediately before or after introduction of a gene editing molecule, or during the time that they are treated with a gene editing molecule and immediately afterwards. In certain embodiments, the plant cell or plant protoplast cultures are exposed to HDR promoting agents, a composition or culture media comprising the HDR promoting agents, or to the HDR promoting agents and aforementioned hypoxic conditions, ROS scavenging agents, and/or Ca 2+ concentrations the before and/or during the time that they are treated with a gene editing molecule and/or immediately afterwards. Exposure of the plant cell or plant protoplast the HDR promoting agents, a composition or culture media comprising the HDR promoting agents, or to the HDR promoting agents and aforementioned hypoxic conditions, ROS scavenging agents, and/or Ca 2+ concentrations can be for about 1, 2, 4, 6, or 8 to about 12, 18, 24, 36, or 48 hours after introduction of a gene editing molecule. Gene editing molecules can be introduced by methods that include transfection, Agrobacterium-mediated transformation, Agro-infection, electroporation, and the like. In certain embodiments, the plant cell or plant protoplast is maintained at a temperature of about 30° C., 32° C., 34° C., or 36° C. to about 38° C., 40° C., or 42° C. for at least about 30, 40, 50, or 60 minutes, or for about 30, 40, 50, 60, to about 70, 80, 90, or 120 minutes, following introduction of the gene editing molecules

Eukaryotic cells (e.g., plant cells) having increased Homology Directed Repair (HDR)-mediated genome modification frequencies conferred by exposure to HDR promoting agents (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) and/or are provided herein. Also provided by the disclosure are compositions or compositions derived from or grown from the plant cell or plant protoplast having increased HDR-mediated genome modification frequencies provided by the systems and methods disclosed herein. In certain embodiments, such compositions include multiple protoplasts or cells, callus, a somatic embryo, a somatic meristem, embryogenic callus, or a regenerated plant grown from the plant cell or plant protoplast having increased HDR-mediated genome modification frequencies; wherein the HDR promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) is provided at an effective concentration. Increased HDR-mediated genome modification frequencies in cells that have been exposed to HDR promoting agents can be assessed by a variety of techniques. In certain embodiments, such techniques can compare the frequency of HDR observed in cells exposed to the HDR promoting agents versus the frequency of HDR in control cells that were not exposed to HDR promoting agent.

In certain embodiments, the eukaryotic cells (e.g., plant cells) used in the systems, methods, and compositions provided herein can include non-dividing cells. Such non-dividing cells can include plant cell protoplasts, eukaryotic cells subjected to one or more of a genetic and/or pharmaceutically-induced cell-cycle blockage, and the like. In certain embodiments, the non-dividing cells can be induced to divide (e.g., by reversing or removing a genetic or pharmaceutical cell-cycle blockages) following treatment with the HDR-promoting agents (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof).

In certain embodiments, the eukaryotic cells (e.g., plant cells) in used in the systems, methods, and compositions provided herein can include dividing cells. Dividing cells can include those cells found in various plant tissues including leaves, meristems, and embryos. These tissues include, but are not limited to dividing cells from young maize leaf, meristems and scutellar tissue from about 8 or 10 to about 12 or 14 days after pollination (DAP) embryos. The isolation of maize embryos has been described in several publications (Brettschneider, Becker, and Lörz 1997; Leduc et al. 1996; Frame et al. 2011; K. Wang and Frame 2009). In certain embodiments, basal leaf tissues (e.g., leaf tissues located about 0 to 3 cm from the ligule of a maize plant; Kirienko, Luo, and Sylvester 2012) are targeted for HDR-mediated gene editing. Methods for obtaining regenerable plant structures and regenerating plants from the HDR-mediated gene editing of plant cells provided herein can be adapted from methods disclosed in US Patent Application Publication No. 20170121722, which is incorporated herein by reference in its entirety and specifically with respect to such disclosure. In certain embodiments, single plant cells subjected to the HDR-mediated gene editing will give rise to single regenerable plant structures. In certain embodiments, the single regenerable plant cell structure can form from a single cell on, or within, an explant that has been subjected to the HDR-mediated gene editing.

In some embodiments, methods provided herein can include the additional step of growing or regenerating a plant from a plant cell that had been subjected to the improved HDR-mediated gene editing or from a regenerable plant structure obtained from that plant cell. In certain embodiments, the plant can further comprise an inserted transgene, a target gene edit, or genome edit as provided by the methods and compositions disclosed herein. In certain embodiments, callus is produced from the plant cell, and plantlets and plants produced from such callus. In other embodiments, whole seedlings or plants are grown directly from the plant cell without a callus stage. Thus, additional related aspects are directed to whole seedlings and plants grown or regenerated from the plant cell or plant protoplast having a target gene edit or genome edit, as well as the seeds of such plants. In certain embodiments wherein the plant cell or plant protoplast is subjected to genetic modification (for example, genome editing by means of, e.g., an RNA-guided DNA nuclease), the grown or regenerated plant exhibits a phenotype associated with the genetic modification. In certain embodiments, the grown or regenerated plant includes in its genome two or more genetic or epigenetic modifications that in combination provide at least one phenotype of interest. In certain embodiments, a heterogeneous population of plant cells having a target gene edit or genome edit, at least some of which include at least one genetic or epigenetic modification, is provided by the method; related aspects include a plant having a phenotype of interest associated with the genetic or epigenetic modification, provided by either regeneration of a plant having the phenotype of interest from a plant cell or plant protoplast selected from the heterogeneous population of plant cells having a target gene or genome edit, or by selection of a plant having the phenotype of interest from a heterogeneous population of plants grown or regenerated from the population of plant cells having a target gene edit or genome edit. Examples of phenotypes of interest include herbicide resistance, improved tolerance of abiotic stress (e.g., tolerance of temperature extremes, drought, or salt) or biotic stress (e.g., resistance to nematode, bacterial, or fungal pathogens), improved utilization of nutrients or water, modified lipid, carbohydrate, or protein composition, improved flavor or appearance, improved storage characteristics (e.g., resistance to bruising, browning, or softening), increased yield, altered morphology (e.g., floral architecture or color, plant height, branching, root structure). In an embodiment, a heterogeneous population of plant cells having a target gene edit or genome edit (or seedlings or plants grown or regenerated therefrom) is exposed to conditions permitting expression of the phenotype of interest; e.g., selection for herbicide resistance can include exposing the population of plant cells having a target gene edit or genome edit (or seedlings or plants grown or regenerated therefrom) to an amount of herbicide or other substance that inhibits growth or is toxic, allowing identification and selection of those resistant plant cells (or seedlings or plants) that survive treatment. Methods for obtaining regenerable plant structures and regenerating plants from plant cells or regenerable plant structures can be adapted from published procedures (Roest and Gilissen, Acta Bot. Neerl., 1989, 38(1), 1-23; Bhaskaran and Smith, Crop Sci. 30(6):1328-1337; Ikeuchi et al., Development, 2016, 143: 1442-1451). Methods for obtaining regenerable plant structures and regenerating plants from plant cells or regenerable plant structures can also be adapted from US Patent Application Publication No. 20170121722, which is incorporated herein by reference in its entirety and specifically with respect to such disclosure. Also provided are heterogeneous populations, arrays, or libraries of such plants, succeeding generations or seeds of such plants grown or regenerated from the plant cells or plant protoplasts, having a target gene edit or genome edit, parts of the plants (including plant parts used in grafting as scions or rootstocks), or products (e.g., fruits or other edible plant parts, cleaned grains or seeds, edible oils, flours or starches, proteins, and other processed products) made from the plants or their seeds. Embodiments include plants grown or regenerated from the plant cells having a target gene edit or genome edit, wherein the plants contain cells or tissues that do not have a genetic or epigenetic modification, e.g., grafted plants in which the scion or rootstock contains a genetic or epigenetic modification, or chimeric plants in which some but not all cells or tissues contain a genetic or epigenetic modification. Plants in which grafting is commonly useful include many fruit trees and plants such as many citrus trees, apples, stone fruit (e.g., peaches, apricots, cherries, and plums), avocados, tomatoes, eggplant, cucumber, melons, watermelons, and grapes as well as various ornamental plants such as roses. Grafted plants can be grafts between the same or different (generally related) species. Additional related aspects include a hybrid plant provided by crossing a first plant grown or regenerated from a plant cell or plant protoplast having a target gene edit or genome edit and having at least one genetic or epigenetic modification, with a second plant, wherein the hybrid plant contains the genetic or epigenetic modification; also contemplated is seed produced by the hybrid plant. Also envisioned as related aspects are progeny seed and progeny plants, including hybrid seed and hybrid plants, having the regenerated plant as a parent or ancestor. The plant cells and derivative plants and seeds disclosed herein can be used for various purposes useful to the consumer or grower. The intact plant itself may be desirable, e.g., plants grown as cover crops or as ornamentals. In other embodiments, processed products are made from the plant or its seeds, such as extracted proteins, oils, sugars, and starches, fermentation products, animal feed or human food, wood and wood products, pharmaceuticals, and various industrial products.

An HDR promoting agent can be provided to a eukaryotic cell (e.g., a plant cell or plant protoplast) in the methods, systems, and compositions provided herein by any suitable technique. In certain embodiments, the HDR promoting agent is provided by directly contacting a cell with the HDR promoting agent. In certain embodiments, the HDR promoting agent is provided by transporting the HDR promoting agent into a cell using a chemical, enzymatic, or physical agent.

In certain embodiments of the methods, systems, cells, and compositions provided herein, transient expression of the genome editing molecules is used. Transient expression of genome editing molecules can be achieved by a variety of techniques. In certain embodiments, the genome editing molecules are provided directly to the cells, systems, methods, and compositions as isolated molecules, as isolated or semi-purified products of a cell free synthetic process (e.g., in vitro translation), or as isolated or semi-purified products of in a cell-based synthetic process (e.g., such as in a bacterial or other cell lysate). In certain embodiments, genome editing molecules are targeted to the cell or cell nucleus in a manner that insures transient expression (e.g., by methods adapted from Gao et al. 2016; or Li et al. 2009). In certain embodiments, the genome editing molecules are delivered into the cell by delivery of the genome editing molecule in the absence of any polynucleotide that encodes the genome editing molecule. Examples of exogenous genome editing molecules that can be delivered in the absence of any encoding polynucleotides include sequence-specific endonucleases, and RNA guides. RNA-guided DNA binding polypeptide/RNA guides can be delivered separately and/or as RNP complexes. In certain embodiments, gene editing molecules can be produced in a heterologous system, purified and delivered to plant cells by particle bombardment (e.g., by methods adapted from Martin-Ortigosa and Wang 2014). In embodiments where the gene editing molecules are delivered in the absence of any encoding polynucleotides, the delivered agent is expected to degrade over time in the absence of ongoing expression from any introduced encoding polynucleotides to result in transient expression. In certain embodiments, the genome editing molecules can be delivered into the cell by delivery of a polynucleotide that encodes the genome editing molecules. In certain embodiments, genome editing molecules can be encoded on a bacterial plasmid and delivered to plant tissue by particle bombardment (e.g., by methods adapted from Hamada et al. 2018; or Kirienko, Luo, and Sylvester 2012). In certain embodiments, genome editing molecules can be encoded on a T-DNA and transiently transferred to plant cells using Agrobacterium (e.g., by methods adapted from Leonelli et al. 2016; or Wu et al. 2014). In certain embodiments, genome editing molecules can be encoded in a viral genome and delivered to plants (e.g., by methods adapted from Honig et al. 2015). In certain embodiments, genome editing molecules can be encoded in mRNA or an RNA comprising an internal ribosome entry site (IRES) and delivered to target cells. In certain embodiments where the genome editing molecules comprise an RNA-guided DNA binding polypeptide and an RNA guide, the polypeptide or guide can be delivered by a combination of: (i) an encoding polynucleotide for either polypeptide or the guide; and (ii) either the polypeptide or the guide itself in the absence of an encoding polynucleotide. In certain embodiments, the polynucleotide that encodes the genome editing molecules is not integrated into a plant cell genome (e.g., as a polynucleotide lacking sequences that provide for integration, by agroinfiltration on an integration deficient T-DNA vector or system, or in a viral vector), is not operably linked to polynucleotides which provide for autonomous replication, and/or only provided with factors (e.g., viral replication proteins) that provide for autonomous replication. Suitable techniques for transient expression including biolistic and other micro- or nanoparticulate-mediated delivery of polynucleotides, agroinfiltration, and use of viral vectors as disclosed by Canto, 2016 and others can be adapted for transient expression of the genome editing molecules provided herein. Transient expression of the genome editing molecules encoded by a non-integrated polynucleotide can be effectuated by excision of the polynucleotide and/or regulated expression of the genome editing molecules. In certain embodiments, the polynucleotide that encodes the gene editing molecules is integrated into a eukaryotic cell genome (e.g., a plant nuclear or plastid genome) and transient expression of the agent is effectuated by excision of the polynucleotide and/or regulated expression of the gene editing molecules. Excision of a polynucleotide encoding the gene editing molecules can be provided by use of site-specific recombination systems (e.g., Cre-Lox, FLP-FRT). Regulated expression of the gene editing molecules can be effectuated by methods including: (i) operable linkage of the polynucleotide encoding the gene editing molecules to a developmentally regulated, de-repressable, and/or inducible promoter; and/or (ii) introduction of a polynucleotide (e.g., dsRNA or a miRNA) that can induce siRNA-mediated inhibition of the genome editing molecules. Suitable site-specific recombination systems as well as developmentally regulated, de-repressable, and/or inducible promoters include those disclosed in US Patent Application Publication No. 20170121722, which is incorporated herein by reference in its entirety and specifically with respect to such disclosure.

Polynucleotides that can be used to effectuate transient expression of genome editing molecules (e.g., a polynucleotide encoding a sequence-specific endonuclease, RNA-guided endonuclease, and/or a guide RNA) include: (a) double-stranded RNA; (b) single-stranded RNA; (c) chemically modified RNA; (d) double-stranded DNA; (e) single-stranded DNA; (f) chemically modified DNA; or (g) a combination of any of (a)-(f). Certain embodiments of the polynucleotide further include additional nucleotide sequences that provide useful functionality; non-limiting examples of such additional nucleotide sequences include an aptamer or riboswitch sequence, nucleotide sequence that provides secondary structure such as stem-loops or that provides a sequence-specific site for an enzyme (e.g., a sequence-specific recombinase or endonuclease site), T-DNA (e.g., DNA sequence encoding a genome editing molecule is enclosed between left and right T-DNA borders from Agrobacterium spp. or from other bacteria that infect or induce tumors in plants), a DNA nuclear-targeting sequence, a regulatory sequence such as a promoter sequence, and a transcript-stabilizing or -destabilizing sequence. Certain embodiments of the polynucleotides comprising gene-editing molecules include those wherein the polynucleotide is complexed with, or covalently or non-covalently bound to, a non-nucleic acid element, e.g., a carrier molecule, an antibody, an antigen, a viral movement protein, a cell-penetrating or pore-forming peptide, a polymer, a detectable label, a quantum dot, or a particulate or nanoparticulate.

Various treatments are useful in delivery of gene editing molecules and/or an HDR-promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) to a eukaryotic cell (e.g., a plant cell). In certain embodiments, one or more treatments is employed to deliver the gene editing molecules and/or an HDR promoting agent (e.g., comprising a polynucleotide, polypeptide, compound, or combination thereof) into a eukaryotic or plant cell, e.g., through barriers such as a cell wall, a plasma membrane, a nuclear envelope, and/or other lipid bilayer. In certain embodiments, a composition comprising the HDR promoting agent(s) are delivered directly, for example by direct contact of the composition with a eukaryotic cell. Aforementioned compositions can be provided in the form of a liquid, a solution, a suspension, an emulsion, a reverse emulsion, a colloid, a dispersion, a gel, liposomes, micelles, an injectable material, an aerosol, a solid, a powder, a particulate, a nanoparticle, or a combination thereof can be applied directly to a eukaryotic cell, eukaryotic tissue, eukaryotic organ, eukaryotic organism, plant, plant part, plant cell, or plant explant (e.g., through abrasion or puncture or otherwise disruption of the cell wall or cell membrane, by spraying or dipping or soaking or otherwise directly contacting, by microinjection). For example, a plant cell or plant protoplast is soaked in a liquid composition comprising the HDR promoting agent, whereby the agent is delivered to the plant cell. In certain embodiments, the agent-containing composition is delivered using negative or positive pressure, for example, using vacuum infiltration or application of hydrodynamic or fluid pressure. In certain embodiments, the HDR promoting agent-containing composition is introduced into a plant cell or plant protoplast, e.g., by microinjection or by disruption or deformation of the cell wall or cell membrane, for example by physical treatments such as by application of negative or positive pressure, shear forces, or treatment with a chemical or physical delivery agent such as surfactants, liposomes, or nanoparticles; see, e.g., delivery of materials to cells employing microfluidic flow through a cell-deforming constriction as described in US Published Patent Application 2014/0287509, incorporated by reference in its entirety herein. Other techniques useful for delivering the agent-containing composition to a eukaryotic cell, plant cell or plant protoplast include: ultrasound or sonication; vibration, friction, shear stress, vortexing, cavitation; centrifugation or application of mechanical force; mechanical cell wall or cell membrane deformation or breakage; enzymatic cell wall or cell membrane breakage or permeabilization; abrasion or mechanical scarification (e.g., abrasion with carborundum or other particulate abrasive or scarification with a file or sandpaper) or chemical scarification (e.g., treatment with an acid or caustic agent); and electroporation. In certain embodiments, the agent-containing composition is provided by bacterially mediated (e.g., Agrobacterium sp., Rhizobium sp., Sinorhizobium sp., Mesorhizobium sp., Bradyrhizobium sp., Azobacter sp., Phyllobacterium sp.) transfection of the plant cell or plant protoplast with a polynucleotide encoding the agent (e.g., sequence-specific endonuclease, and/or guide RNA); see, e.g., Broothaerts et al. (2005) Nature, 433:629-633. Any of these techniques or a combination thereof are alternatively employed on the plant explant, plant part or tissue or intact plant (or seed) from which a plant cell is optionally subsequently obtained or isolated; in certain embodiments, the agent-containing composition is delivered in a separate step after the plant cell has been isolated. In certain embodiments, the aforementioned methods can also be used to introduce a genome editing molecule into the eukaryotic cell (e.g., plant cell).

In embodiments, a treatment employed in delivery of an HDR-promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) to a eukaryotic cell (e.g., plant cell) is carried out under a specific thermal regime, which can involve one or more appropriate temperatures, e.g., chilling or cold stress (exposure to temperatures below that at which normal plant growth occurs), or heating or heat stress (exposure to temperatures above that at which normal plant growth occurs), or treating at a combination of different temperatures. In certain embodiments, a specific thermal regime is carried out on the plant cell, or on a plant, plant explant, or plant part from which a plant cell or plant protoplast is subsequently obtained or isolated, in one or more steps separate from the HDR promoting agent delivery. In certain embodiments, the aforementioned methods can also be used to introduce a genome editing molecule into the eukaryotic cell.

In certain embodiments of the plant parts, systems, methods, and compositions provided herein, a whole plant or plant part or seed, or an isolated plant cell, a plant explant, or the plant or plant part from which a plant cell or plant protoplast is obtained or isolated, is treated with one or more delivery agents which can include at least one chemical, enzymatic, or physical agent, or a combination thereof. In certain embodiments, a composition comprising an HDR promoting agent further includes one or more than one chemical, enzymatic, or physical agents for delivery. Treatment with the chemical, enzymatic or physical agent can be carried out simultaneously with the agent delivery or in one or more separate steps that precede or follow the agent delivery. In certain embodiments, a chemical, enzymatic, or physical agent, or a combination of these, is associated or complexed with the HDR promoting agent; examples of such associations or complexes include those involving non-covalent interactions (e.g., ionic or electrostatic interactions, hydrophobic or hydrophilic interactions, formation of liposomes, micelles, or other heterogeneous composition) and covalent interactions (e.g., peptide bonds, bonds formed using cross-linking agents). In non-limiting examples, the HDR promoting agent is provided as a liposomal complex with a cationic lipid; and/or the HDR promoting agent is provided as a complex with a carbon nanotube. Examples of agents useful for delivering the HDR promoting agents include the various cationic liposomes and polymer nanoparticles reviewed by Zhang et al. (2007) J. Controlled Release, 123:1-10, and the cross-linked multilamellar liposomes described in US Patent Application Publication 2014/0356414 A1, incorporated by reference in its entirety herein. In any of the aforementioned embodiments, it is further contemplated that the aforementioned methods can also be used to introduce a genome editing molecule into the eukaryotic cell (e.g., plant cell).

In certain embodiments, the compositions used in the methods, systems, and compositions that comprise an HDR promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) or gene-editing molecules can further include one or more chemical agents such as:

(a) solvents (e.g., water, dimethylsulfoxide, dimethylformamide, acetonitrile, N-pyrrolidine, pyridine, hexamethylphosphoramide, alcohols, alkanes, alkenes, dioxanes, polyethylene glycol, and other solvents miscible or emulsifiable with water or that will dissolve the HDR promoting agent in non-aqueous systems); (b) fluorocarbons (e.g., perfluorodecalin, perfluoromethyldecalin); (c) glycols or polyols (e.g., propylene glycol, polyethylene glycol); (d) surfactants, including cationic surfactants, anionic surfactants, non-ionic surfactants, and amphiphilic surfactants, e.g., alkyl or aryl sulfates, phosphates, sulfonates, or carboxylates; primary, secondary, or tertiary amines: quaternary ammonium salts; sultaines, betaines; cationic lipids; phospholipids; tallowamine; bile acids such as cholic acid; long chain alcohols; organosilicone surfactants including nonionic organosilicone surfactants such as trisiloxane ethoxylate surfactants or a silicone polyether copolymer such as a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypolypropylene glycol methylether (commercially available as SILWET L-77™ brand surfactant having CAS Number 27306-78-1 and EPA Number CAL. REG. NO. 5905-50073-AA, Momentive Performance Materials, Inc., Albany, N.Y.); specific examples of useful surfactants include sodium lauryl sulfate, the Tween series of surfactants, Triton-X100, Triton-X114, CHAPS and CHAPSO, Tergitol-type NP-40, Nonidet P-40; (e) lipids, lipoproteins, lipopolysaccharides; (f) acids, bases, caustic agents; (g) peptides, proteins, or enzymes (e.g., cellulase, pectolyase, maceroenzyme, pectinase), including cell-penetrating or pore-forming peptides (e.g., (BO100)2K8, Genscript; poly-lysine, poly-arginine, or poly-homoarginine peptides; gamma zein, see US Patent Application publication 2011/0247100, incorporated herein by reference in its entirety; transcription activator of human immunodeficiency virus type 1 (“HIV-1 Tat”) and other Tat proteins, see, e.g., www[dot]lifetein[dot]com/Cell_Penetrating_Peptides[dot]html and Järver (2012) Mol. Therapy—Nucleic Acids, 1:e27, 1-17); octa-arginine or nona-arginine; poly-homoarginine (see Unnamalai et al. (2004) FEBS Letters, 566:307-310); see also the database of cell-penetrating peptides CPPsite 2.0 publicly available at crdd[dot]osdd[dot]net/raghava/cppsite/(h) (h) RNase inhibitors; (i) cationic branched or linear polymers such as chitosan, poly-lysine, DEAE-dextran, polyvinylpyrrolidone (“PVP”), or polyethylenimine (“PEI”, e.g., PEI, branched, MW 25,000, CAS #9002-98-6; PEI, linear, MW 5000, CAS #9002-98-6; PEI linear, MW 2500, CAS #9002-98-6); (j) dendrimers (see, e.g., US Patent Application Publication 2011/0093982, incorporated herein by reference in its entirety); (k) counter-ions, amines or polyamines (e.g., spermine, spermidine, putrescine), osmolytes, buffers, and salts (e.g., calcium phosphate, ammonium phosphate); (l) polynucleotides (e.g., non-specific double-stranded DNA, salmon sperm DNA); (m) transfection agents (e.g., Lipofectin®, Lipofectamine®, and Oligofectamine®, and Invivofectamine® (all from Thermo Fisher Scientific, Waltham, Mass.), PepFect (see Ezzat et al. (2011) Nucleic Acids Res., 39:5284-5298), Transit® transfection reagents (Mirus Bio, LLC, Madison, Wis.), and poly-lysine, poly-homoarginine, and poly-arginine molecules including octo-arginine and nono-arginine as described in Lu et al. (2010) J. Agric. Food Chem., 58:2288-2294); (n) antibiotics, including non-specific DNA double-strand-break-inducing agents (e.g., phleomycin, bleomycin, talisomycin); and/or (o) antioxidants (e.g., glutathione, dithiothreitol, ascorbate). In any of the aforementioned embodiments, it is further contemplated that the aforementioned chemical agents can also be used to introduce a genome editing molecule into the eukaryotic cell (e.g., plant cell).

In certain embodiments, the compositions used in the methods, systems, and compositions that comprise an HDR promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof) are provided to a plant cell in a composition comprising an agriculturally acceptable adjuvant and/or an agriculturally acceptable excipient. Agriculturally acceptable adjuvants include agents that facilitate mixing, application, uptake and/or bioactivity (e.g., increased HDR frequencies) of compositions comprising an HDR promoting agent. Such adjuvants include pH buffering agents, antifoam agents, and drift control agents, surfactants, crop oil concentrates, nitrogen fertilizers (e.g., urea-ammonium nitrates, ammonium sulfates, ammonium nitrates and ammonium polyphosphates), spreader-stickers, wetting agents, humectants (e.g., glycerol, propylene glycol, diethylene glycol, polyethylene glycol), and penetrants. Useful surfactants that can be used include any of the aforementioned cationic surfactants, anionic surfactants, non-ionic surfactants, and amphiphilic surfactants. Useful crop oil concentrates include mixtures of a non-phytotoxic oil at about 80% to 90% by weight or volume and surfactant(s) at about 20% to 1% by weight or volume. Non-phytotoxic oils include petroleum oils, petroleum oil concentrates (e.g., paraffinic and napthalenic oils) and vegetable oils (e.g., triglycerides or methylated oils). Agriculturally acceptable excipients include agents that are essentially inert but function as bulking agents and/or carriers. Agricultural excipients suitable for solid compositions include natural clays, kaolin, pyrophyllite, bentonite, alumina, montmorillonite, kieselguhr, chalk, diatomaceous earths, calcium phosphates, pumice, attapulgite clays, fuller's earth, ground corn cobs, sands, silicates, sodium, calcium or magnesium carbonates, sodium bicarbonate, magnesium sulphate, lime, flours, talc, polysaccharides and other organic and inorganic solid carriers. Agricultural excipients suitable for liquid compositions include water, oil and water emulsions, organic solvents, and the like.

In certain embodiments, the chemical agent is provided simultaneously with the HDR promoting agent (e.g., as a composition comprising a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof and any of the aforementioned chemical agents). In certain embodiments, HDR promoting agent is is non-covalently linked or complexed with one or more chemical agents; for example, an HDR promoting agent can be non-covalently complexed with cationic lipids, polycations (e.g., polyamines), or cationic polymers (e.g., PEI). In certain embodiments, the HDR promoting agent is complexed with one or more chemical agents to form, e.g., a solution, liposome, micelle, emulsion, reverse emulsion, suspension, colloid, or gel. In any of the aforementioned embodiments, it is further contemplated that genome editing molecules comprising polynucleotides and/or polypeptides can be also be delivered as described above.

In certain embodiments, the physical agent for delivery of gene editing molecules is at least one selected from the group consisting of particles or nanoparticles (e.g., particles or nanoparticles made of materials such as carbon, silicon, silicon carbide, gold, tungsten, polymers, or ceramics) in various size ranges and shapes, magnetic particles or nanoparticles (e.g., silenceMag Magnetotransfection agent, OZ Biosciences, San Diego, Calif.), abrasive or scarifying agents, needles or microneedles, matrices, and grids. In certain embodiments, particulates and nanoparticulates are useful in delivery of the gene editing molecules. Useful particulates and nanoparticles include those made of metals (e.g., gold, silver, tungsten, iron, cerium), ceramics (e.g., aluminum oxide, silicon carbide, silicon nitride, tungsten carbide), polymers (e.g., polystyrene, polydiacetylene, and poly(3,4-ethylenedioxythiophene) hydrate), semiconductors (e.g., quantum dots), silicon (e.g., silicon carbide), carbon (e.g., graphite, graphene, graphene oxide, or carbon nanosheets, nanocomplexes, or nanotubes), and composites (e.g., polyvinylcarbazoleigraphene, polystyrene/graphene, platinum/graphene, palladium/graphene nanocomposites). In certain embodiments, such particulates and nanoparticulates are further covalently or non-covalently functionalized, or further include modifiers or cross-linked materials such as polymers (e.g., linear or branched polyethylenimine, poly-lysine), polynucleotides (e.g., DNA or RNA), polysaccharides, lipids, polyglycols (e.g., polyethylene glycol, thiolated polyethylene glycol), polypeptides or proteins, and detectable labels (e.g., a fluorophore, an antigen, an antibody, or a quantum dot). In various embodiments, such particulates and nanoparticles are neutral, or carry a positive charge, or carry a negative charge. Embodiments of compositions including particulates include those formulated, e.g., as liquids, colloids, dispersions, suspensions, aerosols, gels, and solids. Embodiments include nanoparticles affixed to a surface or support, e.g., an array of carbon nanotubes vertically aligned on a silicon or copper wafer substrate. Embodiments include polynucleotide compositions including particulates (e.g., gold or tungsten or magnetic particles) delivered by a Biolistic-type technique or with magnetic force. The size of the particles used in Biolistics is generally in the “microparticle” range, for example, gold microcarriers in the 0.6, 1.0, and 1.6 micrometer size ranges (see, e.g., instruction manual for the Helios® Gene Gun System, Bio-Rad, Hercules, Calif.; Randolph-Anderson et al. (2015) “Sub-micron gold particles are superior to larger particles for efficient Biolistic® transformation of organelles and some cell types”, Bio-Rad US/EG Bulletin 2015), but successful Biolistics delivery using larger (40 nanometer) nanoparticles has been reported in cultured animal cells; see O'Brian and Lummis (2011) BMC Biotechnol., 11:66-71. Other embodiments of useful particulates are nanoparticles, which are generally in the nanometer (nm) size range or less than 1 micrometer, e.g., with a diameter of less than about 1 nm, less than about 3 nm, less than about 5 nm, less than about 10 nm, less than about 20 nm, less than about 40 nm, less than about 60 nm, less than about 80 nm, and less than about 100 nm. Specific, non-limiting embodiments of nanoparticles commercially available (all from Sigma-Aldrich Corp., St. Louis, Mo.) include gold nanoparticles with diameters of 5, 10, or 15 nm; silver nanoparticles with particle sizes of 10, 20, 40, 60, or 100 nm; palladium “nanopowder” of less than 25 nm particle size; single-, double-, and multi-walled carbon nanotubes, e.g., with diameters of 0.7-1.1, 1.3-2.3, 0.7-0.9, or 0.7-1.3 nm, or with nanotube bundle dimensions of 2-10 nm by 1-5 micrometers, 6-9 nm by 5 micrometers, 7-15 nm by 0.5-10 micrometers, 7-12 nm by 0.5-10 micrometers, 110-170 nm by 5-9 micrometers, 6-13 nm by 2.5-20 micrometers. In certain embodiments, physical agents for delivery of gene editing molecules can include materials such as gold, silicon, cerium, or carbon, e.g., gold or gold-coated nanoparticles, silicon carbide whiskers, carborundum, porous silica nanoparticles, gelatin/silica nanoparticles, nanoceria or cerium oxide nanoparticles (CNPs), carbon nanotubes (CNTs) such as single-, double-, or multi-walled carbon nanotubes and their chemically functionalized versions (e.g., carbon nanotubes functionalized with amide, amino, carboxylic acid, sulfonic acid, or polyethylene glycol moeities), and graphene or graphene oxide or graphene complexes. Such physical agents that can be adapted for delivery of gene editing molecules include those disclosed in Wong et al. (2016) Nano Lett., 16:1161-1172; Giraldo et al. (2014) Nature Materials, 13:400-409; Shen et al. (2012) Theranosfics, 2:283-294; Kim et al. (2011) Bioconjugate Chem., 22:2558-2567; Wang et al. (2010) J. Am. Chem. Soc. Comm., 132:9274-9276; Zhao et al. (2016) Nanoscale Res. Lett., 11:195-203; and Choi et al. (2016) J. Controlled Release, 235:222-235. See also, for example, the various types of particles and nanoparticles, their preparation, and methods for their use, e.g., in delivering polynucleotides and polypeptides to cells, disclosed in US Patent Application Publications 2010/0311168, 2012/0023619, 2012/0244569, 2013/0145488, 2013/0185823, 2014/0096284, 2015/0040268, 2015/0047074, and 2015/0208663, all of which are incorporated herein by reference in their entirety.

In certain embodiments wherein the gene editing molecules comprise a gRNA (or polynucleotide encoding the gRNA) and/or a donor DNA template is provided in a composition that further includes an RNA-guided nuclease (or a polynucleotide that encodes the same), one or more one chemical, enzymatic, or physical agent can similarly be employed. In certain embodiments, the RNA guide and/or a donor DNA template and RNA-guided nuclease or polynucleotide encoding the same) are provided separately, e.g., in a separate composition. Such compositions can include other chemical or physical agents (e.g., solvents, surfactants, proteins or enzymes, transfection agents, particulates or nanoparticulates), such as those described above as useful in the polynucleotide compositions. For example, porous silica nanoparticles are useful for delivering a DNA recombinase into maize cells; see, e.g., Martin-Ortigosa et al. (2015) Plant Physiol., 164:537-547, and can be adapted to providing a RNA-guided nuclease or polynucleotide encoding the same into a maize or other plant cell. In one embodiment, the polynucleotide composition includes a gRNA and the RNA-guided nuclease, and further includes a surfactant and a cell-penetrating peptide (CPP) which can be operably linked to the. In an embodiment, the polynucleotide composition includes a plasmid or viral vector that encodes both the gRNA and the RNA-guided nuclease, and further includes a surfactant and carbon nanotubes. In an embodiment, the polynucleotide composition includes multiple gRNAs and an mRNA encoding the RNA-guided nuclease, and further includes particles (e.g., gold or tungsten particles), and the polynucleotide composition is delivered to a plant cell or plant protoplast by Biolistics. In any of the aforementioned embodiments, it is further contemplated that other polynucleotides of interest including genome editing molecules can also be delivered before, during, or after delivery of the gRNA and the RNA-guided nuclease.

In certain embodiments, the plant, plant explant, or plant part from which a plant cell is obtained or isolated is treated with one or more chemical, enzymatic, or physical agent(s) in the process of obtaining, isolating, or exposing or treating the plant cell the cell with an HDR promoting agent or a gene editing molecule. In certain embodiments, the plant cell, plant, plant explant, or plant part is treated with an abrasive, a caustic agent, a surfactant such as Silwet L-77 or a cationic lipid, or an enzyme such as cellulase. In any of the aforementioned embodiments, it is further contemplated that other polynucleotides of interest including genome editing molecules can also be delivered before, during, or after delivery of the HDR promoting agents.

In certain embodiments, one or more than one chemical, enzymatic, or physical agent, separately or in combination with (e.g., as a part of) the composition comprising the HDR promoting agent (e.g., a compound of Table 1, a compound of Table 2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof), is provided/applied at a location in the plant or plant part other than the plant location, part, or tissue from which the plant cell is treated, obtained, or isolated. In certain embodiments, the polynucleotide composition is applied to adjacent or distal cells or tissues and is transported (e.g., through the vascular system or by cell-to-cell movement) to the meristem from which plant cells are subsequently isolated. In certain embodiments, the polynucleotide-containing composition is applied by soaking a seed or seed fragment or zygotic or somatic embryo in the composition, whereby the HDR promoting agent is delivered to the plant cell. In certain embodiments, a flower bud or shoot tip is contacted with an HDR promoting agent-containing composition, whereby the polynucleotide is delivered to cells in the flower bud or shoot tip from which desired plant cells are obtained. In certain embodiments, a HDR promoting agent-containing composition is applied to the surface of a plant or of a part of a plant (e.g., a leaf surface), whereby the HDR promoting agents are delivered to tissues of the plant from which desired plant cells are obtained. In certain embodiments a whole plant or plant tissue is subjected to particle- or nanoparticle-mediated delivery (e.g., Biolistics or carbon nanotube or nanoparticle delivery) of a HDR promoting agent-containing composition, whereby the polynucleotide(s) are delivered to cells or tissues from which plant cells are subsequently obtained. In any of the aforementioned embodiments, it is further contemplated that other polynucleotides of interest including genome editing molecules can also be delivered before, during, or after delivery of the HDR promoting agents.

Genome editing molecules include gene editing molecules for inducing a genetic modification in the plant cells having increased HDR-mediated genome modification frequencies provided herein. In certain embodiments, such genome editing molecules can include: (i) a polynucleotide selected from the group consisting of an RNA guide for an RNA-guided nuclease, a DNA encoding an RNA guide for an RNA-guided nuclease; (ii) a nuclease selected from the group consisting of an RNA-guided nuclease, an RNA-guided DNA endonuclease, a type II Cas nuclease, a Cas9, a type V Cas nuclease, a Cas12a, a CasY, a CasX, a Cas12b, a Cas12c, an engineered nuclease, a codon-optimized nuclease, a zinc-finger nuclease (ZFN), a transcription activator-like effector nuclease (TAL-effector nuclease), Argonaute, a meganuclease or engineered meganuclease; (iii) a polynucleotide encoding one or more nucleases capable of effectuating site-specific modification of a target nucleotide sequence; and/or (iv) a donor template DNA molecule. In certain embodiments, at least one delivery agent is selected from the group consisting of solvents, fluorocarbons, glycols or polyols, surfactants; primary, secondary, or tertiary amines and quaternary ammonium salts; organosilicone surfactants; lipids, lipoproteins, lipopolysaccharides; acids, bases, caustic agents; peptides, proteins, or enzymes; cell-penetrating peptides; RNase inhibitors; cationic branched or linear polymers; dendrimers; counter-ions, amines or polyamines, osmolytes, buffers, and salts; polynucleotides; transfection agents; antibiotics; chelating agents such as ammonium oxalate, EDTA, EGTA, or cyclohexane diamine tetraacetate, non-specific DNA double-strand-break-inducing agents; and antioxidants; particles or nanoparticles, magnetic particles or nanoparticles, abrasive or scarifying agents, needles or microneedles, matrices, and grids. In certain embodiments, the eukaryotic cell (e.g., plant cell), system, method, or composition comprising the cells provided herein further includes (a) at least one cell having a Cas9, a Cas12a, a CasY, a CasX, a Cas12b, or a C2c3 nuclease; (b) at least one guide RNA; and (c) optionally, at least one chemical, enzymatic, or physical delivery agent.

Gene editing molecules of use in the cells, systems, methods, compositions, and reaction mixtures provided herein include molecules capable of introducing a double-strand break (“DSB”) in double-stranded DNA, such as in genomic DNA or in a target gene located within the genomic DNA as well as accompanying guide RNA or donor template polynucleotides. Examples of such gene editing molecules include: (a) a nuclease selected from the group consisting of an RNA-guided nuclease, an RNA-guided DNA endonuclease, a type II Cas nuclease, a Cas9, a type V Cas nuclease, a Cas12a, a CasY, a CasX, a Cas12b, a Cas12c, an engineered nuclease, a codon-optimized nuclease, a zinc-finger nuclease (ZFN), a transcription activator-like effector nuclease (TAL-effector nuclease), an Argonaute, and a meganuclease or engineered meganuclease; (b) a polynucleotide encoding one or more nucleases capable of effectuating site-specific alteration (such as introduction of a DSB) of a target nucleotide sequence; (c) a guide RNA (gRNA) for an RNA-guided nuclease, or a DNA encoding a gRNA for an RNA-guided nuclease; and (d) donor template polynucleotides.

CRISPR-type genome editing can be adapted for use in the eukaryotic cells (e.g., plant cells), systems, methods, and compositions provided herein in several ways. CRISPR elements, i.e., gene editing molecules comprising CRISPR endonucleases and CRISPR single-guide RNAs or polynucleotides encoding the same, are useful in effectuating genome editing without remnants of the CRISPR elements or selective genetic markers occurring in progeny. In certain embodiments, the CRISPR elements are provided directly to the eukaryotic cell (e.g., plant cells), systems, methods, and compositions as isolated molecules, as isolated or semi-purified products of a cell free synthetic process (e.g., in vitro translation), or as isolated or semi-purified products of in a cell-based synthetic process (e.g., such as in a bacterial or other cell lysate). In certain embodiments, genome-inserted CRISPR elements are useful in plant lines adapted for use in the systems, methods, and compositions provide herein. In certain embodiments, plants or plant cells used in the systems, methods, and compositions provided herein can comprise a transgene that expresses a CRISPR endonuclease (e.g., a Cas9, a 12a-type or other CRISPR endonuclease). In certain embodiments, one or more CRISPR endonucleases with unique PAM recognition sites can be used. Guide RNAs (sgRNAs or crRNAs and a tracrRNA) to form an RNA-guided endonuclease/guide RNA complex which can specifically bind sequences in the gDNA target site that are adjacent to a protospacer adjacent motif (PAM) sequence. The type of RNA-guided endonuclease typically informs the location of suitable PAM sites and design of crRNAs or sgRNAs. C-rich PAM sites, e.g., 5′-NGG are typically targeted for design of crRNAs or sgRNAs used with Cas9 proteins. T-rich PAM sites (e.g., 5′-TTTV [1], where “V” is A, C, or G) are typically targeted for design of crRNAs or sgRNAs used with Cas12a proteins (e.g., SEQ ID NO:1, 2, and 3). PAM sites including TTN, CTN, TCN, CCN, TTTN, TCTN, TTCN, CTTN, ATTN, TCCN, TTGN, GTTN, CCCN, CCTN, TTAN, TCGN, CTCN, ACTN, GCTN, TCAN, GCCN, and CCGN targeted for design of crRNAs or sgRNAs used with CasJ proteins (e.g., SEQ ID NO:4). Cpf1 endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016/0208243 A1, which is incorporated herein by reference for its disclosure of DNA encoding Cpf1 endonucleases and guide RNAs and PAM sites. Introduction of one or more of a wide variety of CRISPR guide RNAs that interact with CRISPR endonucleases integrated into a plant genome or otherwise provided to a plant is useful for genetic editing for providing desired phenotypes or traits, for trait screening, or for gene editing mediated trait introgression (e.g., for introducing a trait into a new genotype without backcrossing to a recurrent parent or with limited backcrossing to a recurrent parent). Multiple endonucleases can be provided in expression cassettes with the appropriate promoters to allow multiple genome editing in a spatially or temporally separated fashion in either in chromosome DNA or episome DNA.

CRISPR technology for editing the genes of eukaryotes is disclosed in US Patent Application Publications 2016/0138008A1 and US2015/0344912A1, and in U.S. Pat. Nos. 8,697,359, 8,771,945, 8,945,839, 8,999,641, 8,993,233, 8,895,308, 8,865,406, 8,889,418, 8,871,445, 8,889,356, 8,932,814, 8,795,965, and 8,906,616. Cpf1 endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016/0208243 A1. Other CRISPR nucleases useful for editing genomes include Cas12b and Cas12c (see Shmakov et al. (2015) Mol. Cell, 60:385-397) and CasX and CasY (see Burstein et al. (2016) Nature, doi:10.1038/nature21059). Plant RNA promoters for expressing CRISPR guide RNA and plant codon-optimized CRISPR Cas9 endonuclease are disclosed in International Patent Application PCT/US2015/018104 (published as WO 2015/131101 and claiming priority to U.S. Provisional Patent Application 61/945,700). Methods of using CRISPR technology for genome editing in plants are disclosed in US Patent Application Publications US 2015/0082478A1 and US 2015/0059010A1 and in International Patent Application PCT/US2015/038767 A1 (published as WO 2016/007347 and claiming priority to U.S. Provisional Patent Application 62/023,246). All of the patent publications referenced in this paragraph are incorporated herein by reference in their entirety.

For the purposes of gene editing, CRISPR arrays can be designed to contain one or multiple guide RNA sequences corresponding to a desired target DNA sequence; see, for example, Cong et al. (2013) Science, 339:819-823; Ran et al. (2013) Nature Protocols, 8:2281-2308. At least 16 or 17 nucleotides of gRNA sequence are required by Cas9 for DNA cleavage to occur; for Cpf1 at least 16 nucleotides of gRNA sequence are needed to achieve detectable DNA cleavage and at least 18 nucleotides of gRNA sequence were reported necessary for efficient DNA cleavage in vitro; see Zetsche et al. (2015) Cell, 163:759-771. In practice, guide RNA sequences are generally designed to have a length of 17-24 nucleotides (frequently 19, 20, or 21 nucleotides) and exact complementarity (i.e., perfect base-pairing) to the targeted gene or nucleic acid sequence; guide RNAs having less than 100% complementarity to the target sequence can be used (e.g., a gRNA with a length of 20 nucleotides and 1-4 mismatches to the target sequence) but can increase the potential for off-target effects. The design of effective guide RNAs for use in plant genome editing is disclosed in US Patent Application Publication 2015/0082478 A1, the entire specification of which is incorporated herein by reference. More recently, efficient gene editing has been achieved using a chimeric “single guide RNA” (“sgRNA”), an engineered (synthetic) single RNA molecule that mimics a naturally occurring crRNA-tracrRNA complex and contains both a tracrRNA (for binding the nuclease) and at least one crRNA (to guide the nuclease to the sequence targeted for editing); see, for example, Cong et al. (2013) Science, 339:819-823; Xing et al. (2014) BMC Plant Biol., 14:327-340. Chemically modified sgRNAs have been demonstrated to be effective in genome editing; see, for example, Hendel et al. (2015) Nature Biotechnol., 985-991. The design of effective gRNAs for use in plant genome editing is disclosed in US Patent Application Publication 2015/0082478 A1, the entire specification of which is incorporated herein by reference.

Other sequence-specific endonucleases capable of effecting site-specific modification of a target nucleotide sequence in the systems, methods, and compositions provided herein include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TAL-effector nucleases or TALENs), Argonaute proteins, and a meganuclease or engineered meganuclease. Zinc finger nucleases (ZFNs) are engineered proteins comprising a zinc finger DNA-binding domain fused to a nucleic acid cleavage domain, e.g., a nuclease. The zinc finger binding domains provide specificity and can be engineered to specifically recognize any desired target DNA sequence. For a review of the construction and use of ZFNs in plants and other organisms, see, e.g., Urnov et al. (2010) Nature Rev. Genet., 11:636-646. The zinc finger DNA binding domains are derived from the DNA-binding domain of a large class of eukaryotic transcription factors called zinc finger proteins (ZFPs). The DNA-binding domain of ZFPs typically contains a tandem array of at least three zinc “fingers” each recognizing a specific triplet of DNA. A number of strategies can be used to design the binding specificity of the zinc finger binding domain. One approach, termed “modular assembly”, relies on the functional autonomy of individual zinc fingers with DNA. In this approach, a given sequence is targeted by identifying zinc fingers for each component triplet in the sequence and linking them into a multifinger peptide. Several alternative strategies for designing zinc finger DNA binding domains have also been developed. These methods are designed to accommodate the ability of zinc fingers to contact neighboring fingers as well as nucleotide bases outside their target triplet. Typically, the engineered zinc finger DNA binding domain has a novel binding specificity, compared to a naturally-occurring zinc finger protein. Engineering methods include, for example, rational design and various types of selection. Rational design includes, for example, the use of databases of triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, e.g., U.S. Pat. Nos. 6,453,242 and 6,534,261, both incorporated herein by reference in their entirety. Exemplary selection methods (e.g., phage display and yeast two-hybrid systems) are well known and described in the literature. In addition, enhancement of binding specificity for zinc finger binding domains has been described in U.S. Pat. No. 6,794,136, incorporated herein by reference in its entirety. In addition, individual zinc finger domains may be linked together using any suitable linker sequences. Examples of linker sequences are publicly known, e.g., see U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949, incorporated herein by reference in their entirety. The nucleic acid cleavage domain is non-specific and is typically a restriction endonuclease, such as Fokl. This endonuclease must dimerize to cleave DNA. Thus, cleavage by Fokl as part of a ZFN requires two adjacent and independent binding events, which must occur in both the correct orientation and with appropriate spacing to permit dimer formation. The requirement for two DNA binding events enables more specific targeting of long and potentially unique recognition sites. Fokl variants with enhanced activities have been described; see, e.g., Guo et al. (2010) J. Mol. Biol., 400:96-107.

Transcription activator like effectors (TALEs) are proteins secreted by certain Xanthomonas species to modulate gene expression in host plants and to facilitate the colonization by and survival of the bacterium. TALEs act as transcription factors and modulate expression of resistance genes in the plants. Recent studies of TALEs have revealed the code linking the repetitive region of TALEs with their target DNA-binding sites. TALEs comprise a highly conserved and repetitive region consisting of tandem repeats of mostly 33 or 34 amino acid segments. The repeat monomers differ from each other mainly at amino acid positions 12 and 13. A strong correlation between unique pairs of amino acids at positions 12 and 13 and the corresponding nucleotide in the TALE-binding site has been found. The simple relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for the design of DNA binding domains of any desired specificity. TALEs can be linked to a non-specific DNA cleavage domain to prepare sequence-specific endonucleases referred to as TAL-effector nucleases or TALENs. As in the case of ZFNs, a restriction endonuclease, such as Fokl, can be conveniently used. For a description of the use of TALENs in plants, see Mahfouz et al. (2011) Proc. Natl. Acad. Sci. USA, 108:2623-2628 and Mahfouz (2011) GM Crops, 2:99-103.

Argonautes are proteins that can function as sequence-specific endonucleases by binding a polynucleotide (e.g., a single-stranded DNA or single-stranded RNA) that includes sequence complementary to a target nucleotide sequence) that guides the Argonaut to the target nucleotide sequence and effects site-specific alteration of the target nucleotide sequence; see, e.g., US Patent Application Publication 2015/0089681, incorporated herein by reference in its entirety.

Donor template DNA molecules used in the methods, systems, eukaryotic cells (e.g., plant cells), and compositions provided herein include DNA molecules comprising, from 5′ to 3′, a first homology arm, a replacement DNA, and a second homology arm, wherein the homology arms containing sequences that are partially or complete homologous to genomic DNA (gDNA) sequences flanking a target site-specific endonuclease cleavage site in the gDNA and wherein the replacement DNA can comprise an insertion, deletion, or substitution of 1 or more DNA base pairs relative to the target gDNA. In certain embodiments, a donor DNA template homology arm can be about 200, 400, or 600 to about 800, or 1000 base pairs in length. In certain embodiments, a donor template DNA molecule can be delivered to a eukaryotic cell (e.g., a plant cell) in a circular (e.g., a plasmid or a viral vector including a geminivirus vector) or a linear DNA molecule. Donor DNA templates can be synthesized either chemically or enzymatically (e.g., in a polymerase chain reaction (PCR)).

Other genome editing molecules used in plant cells and methods provided herein include transgenes or vectors comprising the same. Such transgenes can confer useful traits that include herbicide tolerance, pest tolerance (e.g., tolerance to insects, nematodes, or plant pathogenic fungi and bacteria), unproved yield, increased and/or qualitatively improved oil, starch, and protein content, improved abiotic stress tolerance (e.g., improved or enhanced water use efficiency or drought tolerance, osmotic stress tolerance, high salinity stress tolerance, heat stress tolerance, enhanced cold tolerance, including cold germination tolerance), and the like. Such transgenes include both transgenes that confer the trait by expression of an exogenous protein as well as transgenes that confer the trait by inhibiting expression of endogenous plant genes (e.g., by inducing an siRNA response which inhibits expression of the endogenous plant genes). Transgenes that can provide such traits are disclosed in US Patent Application Publication Nos. 20170121722 and 20170275636, which are each incorporated herein by reference in their entireties and specifically with respect to such disclosures.

In some embodiments, one or more polynucleotides or vectors driving expression of one or more polynucleotides encoding any of the aforementioned HDR promoting agents and/or genome editing molecules are introduced into a eukaryotic cell (e.g., plant cell). In certain embodiments, a polynucleotide vector comprises a regulatory element such as a promoter operably linked to one or more polynucleotides encoding HDR promoting agents or genome editing molecules. In such embodiments, expression of these polynucleotides can be controlled by selection of the appropriate promoter, particularly promoters functional in a eukaryotic cell (e.g., plant cell); useful promoters include constitutive, conditional, inducible, and temporally or spatially specific promoters (e.g., a tissue specific promoter, a developmentally regulated promoter, or a cell cycle regulated promoter). Developmentally regulated promoters that can be used in plant cells include Phospholipid Transfer Protein (PLTP), fructose-1,6-bisphosphatase protein, NAD(P)-binding Rossmann-Fold protein, adipocyte plasma membrane-associated protein-like protein, Rieske [2Fe-2S] iron-sulfur domain protein, chlororespiratory reduction 6 protein, D-glycerate 3-kinase, chloroplastic-like protein, chlorophyll a-b binding protein 7, chloroplastic-like protein, ultraviolet-B-repressible protein, Soul heme-binding family protein, Photosystem I reaction center subunit psi-N protein, and short-chain dehydrogenase/reductase protein that are disclosed in US Patent Application Publication No. 20170121722, which is incorporated herein by reference in its entirety and specifically with respect to such disclosure. In certain embodiments, the promoter is operably linked to nucleotide sequences encoding multiple guide RNAs, wherein the sequences encoding guide RNAs are separated by a cleavage site such as a nucleotide sequence encoding a microRNA recognition/cleavage site or a self-cleaving ribozyme (see, e.g., Ferré-D'Amaré and Scott (2014) Cold Spring Harbor Perspectives Biol., 2:a003574). In certain embodiments, the promoter is an RNA polymerase III promoter operably linked to a nucleotide sequence encoding one or more guide RNAs. In certain embodiments, the promoter operably linked to one or more polynucleotides is a constitutive promoter that drives gene expression in eukaryotic cells (e.g., plant cells). In certain embodiments, the promoter drives gene expression in the nucleus or in an organelle such as a chloroplast or mitochondrion. Examples of constitutive promoters for use in plants include a CaMV 35S promoter as disclosed in U.S. Pat. Nos. 5,858,742 and 5,322,938, a rice actin promoter as disclosed in U.S. Pat. No. 5,641,876, a maize chloroplast aldolase promoter as disclosed in U.S. Pat. No. 7,151,204, and the nopaline synthase (NOS) and octopine synthase (OCS) promoters from Agrobacterium tumefaciens. In certain embodiments, the promoter operably linked to one or more polynucleotides encoding elements of a genome-editing system is a promoter from figwort mosaic virus (FMV), a RUBISCO promoter, or a pyruvate phosphate dikinase (PPDK) promoter, which is active in photosynthetic tissues. Other contemplated promoters include cell-specific or tissue-specific or developmentally regulated promoters, for example, a promoter that limits the expression of the nucleic acid targeting system to germline or reproductive cells (e.g., promoters of genes encoding DNA ligases, recombinases, replicases, or other genes specifically expressed in germline or reproductive cells). In certain embodiments, the genome alteration is limited only to those cells from which DNA is inherited in subsequent generations, which is advantageous where it is desirable that expression of the genome-editing system be limited in order to avoid genotoxicity or other unwanted effects. All of the patent publications referenced in this paragraph are incorporated herein by reference in their entirety.

Expression vectors or polynucleotides provided herein may contain a DNA segment near the 3′ end of an expression cassette that acts as a signal to terminate transcription and directs polyadenylation of the resultant mRNA, and may also support promoter activity. Such a 3′ element is commonly referred to as a “3′-untranslated region” or “3′-UTR” or a “polyadenylation signal.” In some cases, plant gene-based 3′ elements (or terminators) consist of both the 3′-UTR and downstream non-transcribed sequence (Nuccio et al., 2015). Useful 3′ elements include: Agrobacterium tumefaciens nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, and tr7 3′ elements disclosed in U.S. Pat. No. 6,090,627, incorporated herein by reference, and 3′ elements from plant genes such as the heat shock protein 17, ubiquitin, and fructose-1,6-biphosphatase genes from wheat (Triticum aestivum), and the glutelin, lactate dehydrogenase, and beta-tubulin genes from rice (Oryza sativa), disclosed in US Patent Application Publication 2002/0192813 A1, incorporated herein by reference.

In certain embodiments, a vector or polynucleotide comprising an expression cassette includes additional components, e.g., a polynucleotide encoding a drug resistance or herbicide gene or a polynucleotide encoding a detectable marker such as green fluorescent protein (GFP) or beta-glucuronidase (gus) to allow convenient screening or selection of cells expressing the vector or polynucleotide. Selectable markers include genes that confer resistance to herbicidal compounds, such as glyphosate, sulfonylureas, glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Such selectable marker genes and selective agents include the maize HRA gene (Lee et al., 1988, EMBO J 7:1241-1248) which confers resistance to sulfonylureas and imidazolinones, the CP4 gene that confers resistance to glyphosate (US Reissue Patent RE039247, specifically incorporated herein by reference in its entirety and with respect to such genes and related selection methods), the GAT gene which confers resistance to glyphosate (Castle et al., 2004, Science 304:1151-1154), genes that confer resistance to spectinomycin such as the aadA gene (Swab et al., 1990, Plant Mol Biol. 14:197-205) and the bar gene that confers resistance to glufosinate ammonium (White et al., 1990, Nucl. Acids Res. 25:1062), and PAT (or moPAT for corn, see Rasco-Gaunt et al., 2003, Plant Cell Rep. 21:569-76; also see Sivamani et al., 2019) and the PMI gene that permits growth on mannose-containing medium (Negrotto et al., 2000, Plant Cell Rep. 22:684-690).

In certain embodiments, a counter-selectable marker can be used in the eukaryotic cells (e.g., plant), methods, systems, and compositions provided herein. Such counter-selectable markers can in certain embodiments be incorporated into any DNA that is not intended for insertion into a host cell genome ar target editing sites. In such embodiments, non-limiting examples of DNAs with counter-selectable markers include any DNA molecules that are linked to DNAs encoding gene-editing molecules, and/or donor template DNA molecules. Vectors or DNA molecules comprising donor template DNA molecules wherein the counter-selectable marker is linked to the donor template DNA and optionally separated from the donor template DNA by a target editing site sequence. Examples of counter-selectable markers that can be used in Plants include cytosine deaminase genes (e.g., used in conjunction with 5-fluorocytosine; Schlaman and Hooykaas, 1997), phosphonate ester hydrolases (e.g., used in conjunction with phosphonate esters of glyphosate including glycerol glyphosate; Dotson, et al. 1996), a nitrate reductase (e.g., used in conjunction with chlorate on media containing ammonia as a sole nitrogen source; Nussaume, et al. 1991).

In certain embodiments, the use of a selectable marker is obviated by the increased frequency of HDR provided by the HDR promoting agents (i.e., HDR promoting agents). In such embodiments, a selectable marker and/or a counter-selectable marker can be omitted from any of a donor template DNA molecule, a plasmid used to deliver a donor-template or other DNA molecule, or any other vector (e.g., viral vector) or polynucleotide used in the cells, system, method, or composition provided herein.

EMBODIMENTS

Various embodiments of the eukaryotic cells (e.g., plant cells), systems, and methods provided herein are included in the following non-limiting list of embodiments.

1. A method for increasing Homology Directed Repair (HDR)-mediated genome modification of a plant cell genome, comprising:

-   -   providing genome editing molecules to a plant cell,     -   wherein the plant cell is exposed to an effective concentration         of a composition comprising at least one HDR promoting agent         selected from the group consisting of a 5-substituted         2,4-oxazolidinedione, a 5-substituted 2, 4-thiazolidinedione,         CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS         No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No.         146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No.         872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No.         715934-43-2, any bioactive analog thereof, a plant         cell-compatible salt thereof, an ester thereof, and any         combination thereof;     -   wherein the genome editing molecules comprise an RNA-guided         nuclease or a polynucleotide encoding an RNA-guided nuclease, a         guide RNA or a polynucleotide encoding a guide RNA, and a donor         template DNA molecule;     -   whereby the genome editing molecules modify the plant cell         genome by HDR at a frequency that is increased in comparison to         a control method wherein a control plant cell is provided with         the genome editing molecules but is not exposed to at least one         of said HDR promoting agents or any combination thereof.         2. The method of embodiment 1, wherein the frequency of HDR is         increased by at least 1.5-fold, at least 2-fold, or at least         3-fold in comparison to the control method wherein a control         plant cell is provided with the genome editing molecules but is         not exposed to at least one of said HDR promoting agents or any         combination thereof.         3. The method of embodiment 1 or 2, wherein the plant cell is         haploid, diploid, or polyploid.         4. The method of any one of embodiments 1 to 3, wherein the         plant cell is in a culture medium, in a plant, or in a plant         tissue.         5. The method of any one of embodiments 1 to 4, wherein the         level of at least one oxygen species is lowered in the plant         cell by exposure of the plant cell to a hypoxic condition, or by         exposure of the plant cell to at least one reactive oxygen         species (ROS) concentration lowering agent, or by exposure of         the plant cell to both a hypoxic condition and to at least one         ROS concentration lowering agent.         6. The method of embodiment 5, wherein the hypoxic condition         comprises maintaining the cell in air comprising an oxygen         concentration of about 12% to about 5% oxygen by volume, or         wherein the cell is in a liquid culture medium and the hypoxic         condition comprises maintaining the cell and the medium in air         comprising an oxygen concentration of about 12% to about 5%         oxygen by volume.         7. The method of embodiment 5 or 6, wherein the reactive oxygen         species (ROS) concentration lowering agent comprises an         exogenously provided enzymatic ROS scavenging agent or an         exogenously provided non-enzymatic ROS scavenging agent or a         combination thereof.         8. The method of any one of embodiments 5 to 7, wherein the HDR         promoting agent is selected from the group consisting of a         5-substituted 2,4-oxazolidinedione, a 5-substituted 2,         4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9,         CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS         No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS         No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog         thereof, a plant cell-compatible salt thereof, an ester thereof,         and any combination thereof.         9. The method of embodiment 8, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.         10. The method of any one of embodiments 1 to 4, wherein the         HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.         11. The method of embodiment 10, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5). Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.         12. The method of any one of embodiments 1 to 11, wherein a         bioactive analog thereof is:     -   (i) a substitution of a halogen with another halogen;     -   (ii) a substitution of a C1 to C6 alkyl group or a C1 to C6         alkoxy group with a different C1 to C6 alkyl group or a         different C1 to C6 alkoxy group, respectively;     -   (iii) a substitution of an unsubstituted phenyl group with a         substituted phenyl group, wherein optionally the substitutions         in the phenyl group are selected from a methyl, an alkoxy,         aminoalkyl, or halogen; and/or,     -   (iv) a substitution of a substituted phenyl group with a         different substituted phenyl group wherein optionally the         substitutions in the phenyl group are selected from a methyl, an         alkoxy, aminoalkyl, or halogen.         13. The method of any one of embodiments 1 to 11, wherein the         composition comprising the HDR promoting agent further comprises         an agriculturally acceptable adjuvant and/or excipient.         14. The method of any one of embodiments 1 to 11, wherein the         plant cell is contained or supported by a plant cell culture         medium and Ca2+ and/or Mg2+ is provided in the plant cell         culture medium at a concentration of about 40 mM to 150 mM.         15. The method of any one of embodiments 1 to 11, further         comprising the step of isolating and/or growing a plant cell,         propagule, or plant obtained from the plant cell comprising the         genomic modification, wherein the genome of the plant cell,         propagule, or plant comprises the genomic modification.         16. A system for modification of a plant gene, comprising:     -   (a) a plant cell;     -   (b) at least one HDR promoting agent selected from the group         consisting of a 5-substituted 2,4-oxazolidinedione, a         5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5. CAS         No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No.         940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No.         28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No.         724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any         bioactive analog thereof, a plant cell-compatible salt thereof,         an ester thereof, and any combination thereof; and     -   (c) genome editing molecule(s) comprising: an RNA-guided         nuclease or a polynucleotide encoding an RNA-guided nuclease, a         guide RNA or a polynucleotide encoding a guide RNA, and a donor         template DNA molecule;     -   (d) wherein the plant cell is associated with, contacts, and/or         contains an effective amount of the HDR promoting agent and the         genome editing molecule(s).         17. The system of embodiment 16, wherein the plant cell is         haploid, diploid, or polyploid.         18. The system of embodiment 16 or 17, wherein the plant cell is         in a culture medium, in a plant, or in a plant tissue.         19. The system of any one of embodiments 16 to 18, wherein the         level of at least one oxygen species is lowered in the plant         cell by exposure of the plant cell to a hypoxic condition, or by         exposure of the plant cell to at least one reactive oxygen         species (ROS) concentration lowering agent, or by exposure of         the plant cell to both a hypoxic condition and to at least one         ROS concentration lowering agent.         20. The system of embodiment 19, wherein the hypoxic condition         comprises maintaining the cell in air comprising an oxygen         concentration of about 12% to about 5% oxygen by volume, or         wherein the cell is in a liquid culture medium and the hypoxic         condition comprises maintaining the cell and the medium in air         comprising an oxygen concentration of about 12% to about 5%         oxygen by volume.         21. The system of embodiment 19, wherein the reactive oxygen         species (ROS) concentration lowering agent comprises an         exogenously provided enzymatic ROS scavenging agent or an         exogenously provided non-enzymatic ROS scavenging agent or a         combination thereof.         22. The system of any one of embodiments 19 to 21, wherein the         HDR promoting agent is selected from the group consisting of a         5-substituted 2,4-oxazolidinedione, a 5-substituted 2,         4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9,         CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS         No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS         No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog         thereof, a plant cell-compatible salt thereof, an ester thereof,         and any combination thereof.         23. The system of embodiment 22, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.         24. The system of any one of embodiments 16 to 18, wherein the         HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.         25. The system of embodiment 24, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), a bioactive analog thereof, and a plant         cell-compatible salt thereof.         26. The system of any one of embodiments 16 to 25, wherein a         bioactive analog thereof is:     -   (i) a substitution of a halogen with another halogen;     -   (ii) a substitution of a C1 to C6 alkyl group or a C1 to C6         alkoxy group with a different C1 to C6 alkyl group or a         different C1 to C6 alkoxy group, respectively;     -   (iii) a substitution of an unsubstituted phenyl group with a         substituted phenyl group, wherein optionally the substitutions         in the phenyl group are selected from a methyl, an alkoxy,         aminoalkyl, or halogen; and/or,     -   (iv) a substitution of a substituted phenyl group with a         different substituted phenyl group wherein optionally the         substitutions in the phenyl group are selected from a methyl, an         alkoxy, aminoalkyl, or halogen.         27. The system of any one of embodiments 16 to 25, wherein the         plant cell is contained or supported by a plant cell culture         medium and Ca2+ and/or Mg2+ is provided in the plant cell         culture medium at a concentration of about 40 mM to 150 mM.         28. The system of any one of embodiments 16 to 25, wherein the         composition comprising the HDR promoting agent further comprises         an agriculturally acceptable adjuvant and/or excipient.         29. A method for making a plant cell having a genomic         modification, comprising:     -   (a) providing genome editing molecules to a plant cell,         -   wherein the plant cell is exposed to an effective amount of             at least one HDR promoting agent selected from the group             consisting of a 5-substituted 2,4-oxazolidinedione, a             5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5,             CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5,             CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0,             CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No.             872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS             No. 715934-43-2, any bioactive analog thereof, a plant             cell-compatible salt thereof, an ester thereof, and any             combination thereof;         -   wherein the genome editing molecules comprise an RNA-guided             nuclease or a polynucleotide encoding an RNA-guided             nuclease, a guide RNA or a polynucleotide encoding a guide             RNA, and a donor template DNA molecule;     -   (b) whereby the genome editing molecules modify the plant cell         genome by homology directed repair (HDR) at a frequency that is         increased in comparison to a control; and isolating or         propagating a plant cell comprising the genome modification,         thereby making the plant cell having a genomic modification.         30. The method of embodiment 29, wherein the genome modification         comprises homology directed repair (HDR) of the plant cell         genome.         31. The method of embodiment 29 or 30, wherein the frequency of         HDR is increased by at least 1.5-fold, 2-fold, or 3-fold in         comparison to a control method wherein a control plant cell is         provided with the genome editing molecules but is not exposed to         the HDR promoting agent.         32. The method of any one of embodiments 29 to 31, wherein the         plant cell is haploid, diploid, or polyploid.         33. The method of any one of embodiments 29 to 32, wherein the         plant cell is in a culture medium, in a plant, or in a plant         tissue.         34. The method of any one of embodiments 29 to 33, wherein the         level of at least one oxygen species is lowered in the plant         cell by exposure of the plant cell to a hypoxic condition, or by         exposure of the plant cell to at least one reactive oxygen         species (ROS) concentration lowering agent, or by exposure of         the plant cell to both a hypoxic condition and to at least one         ROS concentration lowering agent.         35. The method of embodiment 34, wherein the hypoxic condition         comprises maintaining the cell in air comprising an oxygen         concentration of about 12% to about 5% oxygen by volume, or         wherein the cell is in a liquid culture medium and the hypoxic         condition comprises maintaining the cell and the medium in air         comprising an oxygen concentration of about 12% to about 5%         oxygen by volume.         36. The method of embodiment 34, wherein the reactive oxygen         species (ROS) concentration lowering agent comprises an         exogenously provided enzymatic ROS scavenging agent or an         exogenously provided non-enzymatic ROS scavenging agent or a         combination thereof.         37. The method of any one of embodiments 34 to 36, wherein the         HDR promoting agent is selected from the group consisting of a         5-substituted 2,4-oxazolidinedione, a 5-substituted 2,         4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9,         CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS         No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS         No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog         thereof, a plant cell-compatible salt thereof, an ester thereof,         and any combination thereof.         38. The method of embodiment 37, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.         39. The method of any one of embodiments 29 to 33, wherein the         HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.         40. The method of embodiment 39, wherein the 5-substituted 2,         4-thiazolidinedione is selected from the group consisting of         Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No.         213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone         (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No.         112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone         (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0),         Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.         161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone         (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.         41. The method of any one of embodiments 29 to 40, wherein a         bioactive analog thereof is:     -   (i) a substitution of a halogen with another halogen;     -   (ii) a substitution of a C1 to C6 alkyl group or a C1 to C6         alkoxy group with a different C1 to C6 alkyl group or a         different C1 to C6 alkoxy group, respectively;     -   (iii) a substitution of an unsubstituted phenyl group with a         substituted phenyl group, wherein optionally the substitutions         in the phenyl group are selected from a methyl, an alkoxy,         aminoalkyl, or halogen; and/or,     -   (iv) a substitution of a substituted phenyl group with a         different substituted phenyl group wherein optionally the         substitutions in the phenyl group are selected from a methyl, an         alkoxy, aminoalkyl, or halogen.         42. The method of any one of embodiments 29 to 40, wherein the         plant cell in at least step (a) is contained or supported by a         plant cell culture medium and Ca²⁺ and/or Mg²⁺ is provided in         the plant cell culture medium at a concentration of about 40 mM         to 150 mM.         43. The method of any one of embodiments 29 to 40, wherein the         composition comprising the HDR promoting agent further comprises         an agriculturally acceptable adjuvant and/or excipient.         44. The method of any one of embodiments 29 to 40, further         comprising the step of isolating and/or growing a plant cell,         propagule, or plant obtained from the plant cell comprising the         genomic modification, wherein the genome of the plant cell,         propagule, or plant comprises the genomic modification.         45. The method of any one of embodiments 1 to 15 or 29 to 44,         wherein the effective concentration of the HDR-promoting agent         is about 0.1 μM, 0.25 μM, 0.5 μM, or 1 μM to about 10 μM, 25 μM,         50 μM, 100 μM, or 500 μM.         46. The method of embodiment 45, wherein the effective         concentration of the HDR-promoting agent is about 0.5 μM or 1 μM         to about 10 μM, 25 μM, or 50 μM.         47. The system of any one of embodiments 16 to 28, wherein the         effective concentration of the HDR-promoting agent is about 0.1         μM, 0.25 μM, 0.5 μM, or about 1 μM to about 10 μM, 25 μM, 50 μM,         100 μM, or 500 μM.         48. The system of embodiment 47, wherein the effective         concentration of the HDR-promoting agent is about 0.1 μM, 0.05         μM, or 1 μM to about 10 μM, 25 μM, or 50 μM.         49. The system of any one of embodiments 16 to 28, 47, or 48,         wherein the plant cell is contacted with a ROS concentration         lowering agent, wherein the plant cell is in a hypoxic medium         and/or medium comprising a ROS concentration lowering agent, or         wherein the system is maintained under hypoxic conditions.         50. A composition comprising:     -   (a) a plant cell;     -   (b) at least one HDR promoting agent selected from the group         consisting of a 5-substituted 2,4-oxazolidinedione, a         5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS         No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No.         940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No.         28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No.         724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any         bioactive analog thereof, a plant cell-compatible salt thereof,         an ester thereof, and any combination thereof; and     -   (c) genome editing molecule(s) comprising: an RNA-guided         nuclease or a polynucleotide encoding an RNA-guided nuclease, a         guide RNA or a polynucleotide encoding a guide RNA, and a donor         template DNA molecule;         -   wherein the plant cell is associated with, contacts, and/or             contains an effective amount of the HDR promoting agent and             the genome editing molecule(s).             51. The composition of embodiment 50, wherein the plant cell             is haploid, diploid, or polyploid.             52. The composition of embodiment 50 or 51, wherein the             plant cell is in a culture medium, in a plant, in plant             part, or in a plant tissue.             53. The composition of any one of embodiments 50 to 52,             wherein the plant cell is grown under a hypoxic condition,             or treated with an exogenous reactive oxygen species (ROS)             one reactive oxygen species (ROS) concentration lowering             agent, or both grown under the hypoxic condition and treated             with the ROS scavenging agent.             54. The composition of embodiment 53, wherein the hypoxic             condition comprises maintaining the cell in air comprising             an oxygen concentration of about 12% to about 5% oxygen by             volume, or wherein the cell is in a liquid culture medium             and the hypoxic condition comprises maintaining the cell and             the medium in air comprising an oxygen concentration of             about 12% to about 5% oxygen by volume.             55. The composition of embodiment 53, wherein the reactive             oxygen species (ROS) concentration lowering agent comprises             an exogenously provided enzymatic ROS scavenging agent or an             exogenously provided non-enzymatic ROS scavenging agent or a             combination thereof.             56. The composition of any one of embodiments 53 to 55,             wherein the HDR promoting agent is selected from the group             consisting of a 5-substituted 2,4-oxazolidinedione, a             5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5,             CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0.             CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No.             872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS             No. 715934-43-2, any bioactive analog thereof, a plant             cell-compatible salt thereof, an ester thereof, and any             combination thereof.             57. The composition of embodiment 56, wherein the             5-substituted 2, 4-thiazolidinedione is selected from the             group consisting of Rosiglitazone (CAS No. 122320-73-4),             Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No.             74772-77-3), Lobeglitazone (CAS No. 607723-33-1),             Pioglitazone hydrochloride (CAS No. 112529-15-4),             Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No.             146062-49-9), Darglitazone (CAS No. 141200-24-0),             Englitazone (CAS No. 109229-58-5). Netoglitazone (CAS No.             161600-01-7), Rivoglitazone (CAS No. 185428-18-6),             Balaglitazone (CAS No. 199113-98-9), and a plant             cell-compatible salt thereof.             58. The composition of any one of embodiments 50 to 52,             wherein the HDR-promoting agent is a 5-substituted 2,             4-thiazolidinedione.             59. The composition of embodiment 58, wherein the             5-substituted 2, 4-thiazolidinedione is selected from the             group consisting of Rosiglitazone (CAS No. 122320-73-4),             Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No.             74772-77-3), Lobeglitazone (CAS No. 607723-33-1),             Pioglitazone hydrochloride (CAS No. 112529-15-4),             Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No.             146062-49-9), Darglitazone (CAS No. 141200-24-0),             Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No.             161600-01-7), Rivoglitazone (CAS No. 185428-18-6),             Balaglitazone (CAS No. 199113-98-9), a bioactive analog             thereof, and a plant cell-compatible salt thereof.             60. The composition of any one of embodiments 50 to 59,             wherein a bioactive analog thereof is:     -   (v) a substitution of a halogen with another halogen;     -   (vi) a substitution of a C1 to C6 alkyl group or a C1 to C6         alkoxy group with a different C1 to C6 alkyl group or a         different C1 to C6 alkoxy group, respectively;     -   (vii) a substitution of an unsubstituted phenyl group with a         substituted phenyl group, wherein optionally the substitutions         in the phenyl group are selected from a methyl, an alkoxy,         aminoalkyl, or halogen; and/or,     -   (viii) a substitution of a substituted phenyl group with a         different substituted phenyl group wherein optionally the         substitutions in the phenyl group are selected from a methyl, an         alkoxy, aminoalkyl, or halogen.         61. The composition of any one of embodiments 50 to 60, wherein         the plant cell is contained or supported by a plant cell culture         medium and Ca2+ and/or Mg2+ is provided in the plant cell         culture medium at a concentration of about 40 mM to 150 mM.         62. The composition of any one of embodiments 50 to 61, wherein         the composition comprising the HDR promoting agent further         comprises an agriculturally acceptable adjuvant and/or         excipient.         63. The composition of any one of embodiments 50 to 62, wherein         the effective concentration of the HDR-promoting agent is about         0.1 μM, 0.25 μM, 0.5 μM, or about 1 μM to about 10 μM, 25 μM, 50         μM, 100 μM, or 500 μM.         64. The composition of embodiment 63, wherein the effective         concentration of the HDR-promoting agent is about 0.1 μM, 0.05         μM, or 1 μM to about 10 μM, 25 μM, or 50 μM.         65. A composition comprising:     -   (a) a eukaryotic cell;     -   (b) at least one HDR promoting agent selected from the group         consisting of a 5-substituted 2,4-oxazolidinedione,         5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS         No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No.         28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No.         724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any         bioactive analog thereof, a eukaryotic cell-compatible salt         thereof, an ester thereof, and any combination thereof; and     -   (c) genome editing molecule(s) comprising: an RNA-guided         nuclease or a polynucleotide encoding an RNA-guided nuclease, a         guide RNA or a polynucleotide encoding a guide RNA, and a donor         template DNA molecule;         -   wherein the eukaryotic cell is a plant cell or an animal             cell or a fungal cell or a protist cell; wherein the             eukaryotic cell is associated with, contacts, and/or             contains an effective amount of the HDR promoting agent and             the genome editing molecule(s); and         -   wherein the eukaryotic cell is grown under a hypoxic             condition, or treated with an exogenous reactive oxygen             species (ROS) one reactive oxygen species (ROS)             concentration lowering agent, or both grown under the             hypoxic condition and treated with the ROS scavenging agent.             66. The composition of embodiment 65, wherein the hypoxic             condition comprises maintaining the eukaryotic cell in air             comprising an oxygen concentration of about 12% to about 5%             oxygen by volume, or wherein the eukaryotic cell is in a             liquid culture medium and the hypoxic condition comprises             maintaining the eukaryotic cell and the medium in air             comprising an oxygen concentration of about 12% to about 5%             oxygen by volume.             67. The composition of embodiment 65, wherein the reactive             oxygen species (ROS) concentration lowering agent comprises             an exogenously provided enzymatic ROS scavenging agent or an             exogenously provided non-enzymatic ROS scavenging agent or a             combination thereof.

EXAMPLES Example 1

This example describes the use of small molecules having homology-dependent repair (HDR) promoting activity, including the use of such small molecules in combination with hypoxia to increase HDR efficiency. Experiments were designed to test the effects of small molecules and/or hypoxia on Homology Directed Repair (HDR) and Non-Homologous End Joining (NHEJ) on editing a reporter or endogenous gene.

The tests utilized a “traffic light” BFP-LP4/2A-mCherry reporter as the target gene to be edited. A ribonucleoprotein (RNP) with guide RNA (gRNA) targeting the BFP coding sequence (181-200 bp) was designed to introduce a double strand DNA break at 197 bp; this DNA break can be repaired through NHEJ pathway with a small indel which leads to in-frame expression of mCherry-NLS, or can be repaired through the HDR pathway when providing the donor template which leads to a lbp single nucleotide variant (SNV) and the expression of Blue Fluorescent protein (BFP) to be changed to Green Fluorescent Protein (GFP). The experiments were carried out with protoplasts produced from etiolated leaves of B73 maize grown in the dark for 11 days. The protoplasts were co-transfected with the RNP and donor template along with the reporter plasmid. The small molecules in DMSO were provided to the cells at a final concentration of about 5 micromolar. Control cells were incubated with DMSO in the absence of the small molecules at a final concentration of 0.5% by volume. Transfected cells were incubated 48 hours at 26 degrees Celsius in the dark under either normoxic or hypoxic conditions in the presence and absence of the small molecules, and then harvested for imaging on a fluorescent microscope. Results as averaged relative fluorescence units (RFUs), total protoplast count, and GFP-expressing protoplast count per plate.

In this set of experiments, 81 small molecules effected a general increase in HDR efficiency. Fifty-one of the 81 small molecules showed a higher general increase in HDR efficiency under hypoxic conditions than normoxic conditions. Twenty-eight of the 81 small molecules showed a higher general increase under normoxic condition than hypoxic conditions.

Example 2

This example describes a second set of experiments which investigated the effects of the 81 small molecules previously identified in the “traffic light” screen (Example 1) on HDR efficiency in editing an endogenous gene, the maize (Zea mays) r1-colored1 gene with partial genomic sequence SEQ ID NO: 5. A ribonucleoprotein (RNP) was prepared with a guide RNA designed to edit the promoter located at positions 313-333 of SEQ ID NO:5. A donor template was provided as a dsDNA for HDR repair. The experiments were carried out with protoplasts produced from etiolated leaves of B104 maize grown in the dark for 11 days. The protoplasts were co-transfected with the RNP and donor template. Transfected cells were incubated 48 hours at 26 degrees Celsius in the dark under either normoxic or hypoxic conditions with the indicated negative controls, positive controls, and small molecules and then harvested. The negative controls comprised cells transfected with the RNP only (no donor template). DMSO controls comprised the RNP and donor template and DMSO at a final concentration of 0.5% by volume DMSO. The positive control was a mixture of KU-0060648 (CAS No. 881375-00-4; Fischer Scientific, Waltham, Mass., USA), STL127705 (7-[2-(3,4-dimethoxyphenyl)ethyl]amino-3-(3-fluorophenyl)pyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione); Vitas-M, Champaign, Ill., USA), NU7441 (CAS No. 503468-95-9; Fischer Scientific Waltham, Mass., USA), and SCR7 pyrazine (CAS No. 14892-97-8; Tocris, Minneapolis, Minn., USA) (all at a stock concentration of 5 mM in DMSO) that was provided to the protoplasts at a final concentration of each of the four compounds of 5 μM. Certain positive control compounds have been reported to increase CRISPR-mediated HDR (Robert et al. 2015; Chu et al., 2015). All of the tested small molecules were also provided to the protoplasts at a final concentration of 5 μM of the compound and a final DMSO concentration of 0.1% by volume. Genomic DNA was isolated using KAPA Pure Bead capture (Kapa Biosystem) and the isolated gDNA was used as the template for a PCR with PHUSION FLASH (ThermoFisher). Samples were cleaned with KAPA Pure Bead capture and Illumina libraries were prepared and sequenced on MiSeq.

In this set of experiments 63 small molecules showed a higher general increase in HDR editing of the endogenous target gene. Fifty-one small molecules of the 81 showed a higher general increase in HDR under hypoxic conditions than normoxic conditions. Twelve small molecules of the 81 showed a higher general increase in HDR under normoxic conditions than in hypoxic conditions.

A summary of the results obtained for selected small molecules which increased HDR is provided in the following Table. Small molecules which increased HDR in hypoxic conditions are in boldface.

TABLE 3 Hypoxia Hypoxia St. Normoxia Normoxia Chemical CAS NO. Avg. Dev Avg. St. Dev NEG. CTRL 1 0.06 0.03 2.90 0.33 NEG. CTRL 2 0.02 0.02 0.39 0.05 NEG. CTRL 3 1.26 0.05 0.23 0.17 NEG. CTRL 4 2.56 0.46 0.01 0.01 NEG. CTRL. AVG 1 1.29 1.25 1.04 1.61 DMSO 1 0.81 0.28 1.69 0.35 DMSO 2 1.49 0.12 1.37 0.17 DMSO 3 0.01 0.00 0.00 0.00 DMSO 4 1.40 0.21 3.03 0.58 DMSO 5 0.01 0.00 0.01 0.02 DMSO 6 0.76 0.28 1.29 0.30 DMSO 7 0.03 0.04 5.14 0.28 DMSO AVG 2 0.64 0.65 1.79 1.81 POS. CTRL 1 2.24 0.13 2.51 0.13 POS. CTRL 2 2.80 0.01 2.31 0.18 POS. CTRL 3 3.94 0.20 2.48 0.17 POS. CTRL 4 2.76 0.05 1.78 0.04 POS. CTRL. AVG. 3 2.94 0.72 2.27 0.34 SC-9 102649-78-5 5.11 0.39 2.67 0.39 Pregnanolone 128-20-1 2.52 0.16 4.43 0.27 ML 3403 549505-65-9 4.36 0.43 1.47 0.27 Daminozide 1596-84-5 0.48 0.20 4.57 0.57 Rosiglitazone 122320-73-4 4.97 0.50 3.20 0.37 SB 743921 940929-33-9 2.97 0.22 4.76 0.72 Hydrochloride Ispinesib 336113-53-2 4.04 0.25 3.36 0.22 2-Chloroadenosine 146-77-0 5.00 0.63 2.45 0.16 Edaglitazone 213411-83-7 6.28 0.74 3.56 0.52 IBMX 28822-58-4 4.23 0.33 3.05 0.15 PIM-1 Inhibitor 2 477845-12-8 5.19 0.12 1.37 0.30 Ro 3306 872573-93-8 4.91 0.25 1.64 0.15 STF 31 724741-75-7 5.00 0.67 0.40 0.04 ML 228 1357171-62-0 4.49 0.52 0.46 0.03 MI 14 715934-43-2 7.75 1.54 0.37 0.14 ¹Negative control cells were treated with RNPs only (no donor template). Negative control 1, 2, 3, and 4 averages are for triplicate samples and the standard deviation for the triplicate samples is shown. Negative control average is an average of the Negative Control 1, 2, 3, and 4 average values for each of the hypoxia and normoxia samples. ²DMSO control is RNP and donor template with DMSO at a final concentration of 0.5% by volume. DMSO 1-7 averages are for triplicate samples and the standard deviation for the triplicate samples is shown. DMSO Average is an average of the DMSO 1-7 average values for each of the hypoxia and normoxia samples. ³Positive control is at a final concentration of 5 μM for each compound (KU-0060648, CAS No. 881375-00-4; STL127705 (7-[2-(3,4-dimethoxyphenyl)ethyl]amino}-3-(3-fluorophenyl)pyrimido[4,5-dipyrimidine-2,4(1H,3H)-dione); NU7441 (CAS No. 503468-95-9) and SCR7 pyrazine (CAS No. 14892-97-8). Positive control 1-4 averages are for triplicate samples and the standard deviation for the triplicate samples is shown. Positive control average is an average of the positive control 1-4 average values for each of the hypoxia and normoxia samples.

Example 3. Biological Sequences

This example provides non-limiting embodiments of protein and nucleic acid sequences referred to herein. Biological sequences and their SEQ ID NOs are set forth in Table 4.

TABLE 4 Biological Sequences SEQ ID NO: DESCRIPTION SEQUENCE COMMENTS 1 As Cpf1 MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEED Acidaminococcus sp. (wild type) KARNDHYKELKPIIDRIYKTYADQCLQLVQLDWENLSAAI (As) Cpf1 DSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDA INKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLR SFDKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPK FKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEV FSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEV LNLAIQKNDETAHIIASLPHRFIPLFKQILSDRNTLSFIL EEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSID LTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGK ITKSAKEKVQRSLKHEDINLQEIISAAGKELSEAFKQKTS EILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHL LDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNY ATKKPYSVEKEKLNEQMPTLASGWDVNKEKNNGAILFVKN GLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPD AAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITK EIYDLNNPEKEPKKFQTAYAKKTGDQKGYREALCKWIDFT RDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYH ISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNL HTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSRMKRMAH RLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSD EARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQ AANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVI DSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSV VGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFK SKRTGIAEKAVYQQFEKMLIDKLNCLVLKDYPAEKVGGVL NPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFV DPEVWKTIKNHESRKHELEGEDFLHYDVKTGDFILHEKMN RNLSFQRGLPGEMPAWDIVFEKNETQFDAKGTPFIAGKRI VPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNIL PKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSP VRDLNGVCFDSRFQNPEWPMDADANGAYHIALKGQLLLNH LKESKDLKLQNGISNQDWLAYIQELRN 2 LbCpf1 MSKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVED Lachnospiraceae (wild type) EKRAEDYKGVKKLLDRYYLSFINDVLHSIKLKNLNNYISL bacterium (Lb) FRKKTRTEKENKELENLEINLRKEIAKAFKGNEGYKSLFK Cpf1 KDIIETILPEFLDDKDEIALVNSFNGFTTAFTGFFDNREN MFSEEAKSTSIAFRCINENLTRYISNMDIFEKVDAIEDKH EVQEIKEKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAI IGGFVTESGEKIKGLNEYINLYNQKTKQKLPKFKPLYKQV LSDRESLSFYGEGYTSDEEVLEVFRNTLNKNSEIFSSIKK LEKLFKNFDEYSSAGIFVKNGPAISTISKDIFGEWNVIRD KWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQL QEYADADLSVVEKLKEIIIQKVDEIYKVYGSSEKLFDADF VLEKSLKKNDAVVAIMKDLLDSVKSFENYIKAFFGEGKET NRDESFYGDFVLAYDILLKVDHIYDAIRNYVTQKPYSKDK FKLYFQNPQFMGGWDKDKETDYRATILRYGSKYYLAIMDK KYAKCLQKIDKDDVNGNYEKINYKLLPGPNKMLPKVFFSK KWMAYYNPSEDIQKIYKNGTFKKGDMFNLNDCHKLIDFFK DSISRYPKWSNAYDFNFSETEKYKDIAGFYREVEEQGYKV SFESASKKEVDKLVEEGKLYMFQIYNKDFSDKSHGTPNLH TMYFKLLFDENNHGQIRLSGGAELFMRRASLKKEELVVHP ANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPI AINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLY IVVVDGKGNIVEQYSLNEIINNFNGIRIKTDYHSLLDKKE KERFEARQNWTSIENIKELKAGYISQVVHKICELVEKYDA VIALEDLNSGFKNSRVKVEKQVYQKFEKMLIDKLNYMVDK KSNPCATGGALKGYQITNKFESFKSMSTQNGFIFYIPAWL TSKIDPSTGFVNLLKTKYTSIADSKKFISSFDRIMYVPEE DLFEFALDYKNFSRTDADYIKKWKLYSYGNRIRIFRNPKK NNVFDWEEVCLTSAYKELFNKYGINYQQGDIRALLCEQSD KAFYSSFMALMSLMLQMRNSITGRTDVDFLISPVKNSDGI FYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGQFKK AEDEKLDKVKIAISNKEWLEYAQTSVKH 3 Fn Cpf1 MSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDD Francisella (wild type) EKRAKDYKKAKQIIDKYHQFFIEEILSSVCISEDLLQNYS novicida (Fn) DVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKDSEKFK Cpf1 NLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDIT DIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSII YRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAE ELTFDIDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITK FNTIIGGKFVNGENTKRKGINEYINLYSQQINDKTLKKYK MSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQIA AFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLT DLSQQVFDDYSVIGTAVLEYITQQIAPKNLDNPSKKEQEL IAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRFEEILA NFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAE DDVKAIKDLLDQTNNLLHKLKIFHISQSEDKANILDKDEH FYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLNF ENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKI FDDKAIKENKGEGYKKIVYKLLPGANKMLPKVFFSAKSIK FYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCRKF IDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQ GYKLTFENISESYIDSVVNQGKLYLFQIYNKDFSAYSKGR PNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIPKK ITHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFF HCPITINFKSSGANKFNDEINLLLKEKANDVHILSIDRGE RHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAI EKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYN AIVVEEDLNEGEKRGREKVEKQVYQKLEKMLIEKLNYLVE KDNEEDKTGGVLRAYQLTAPEETEKKMGKQTGITYYVPAG ETSKICPVTGEVNQLYPKYESVSKSQEFFSKEDKICYNLD KGYFEESEDYKNEGDKAAKGKWTIASFGSRLINFRNSDKN HNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGESD KKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNE EDSRQAPKNMPQDADANGAYHIGLKGLMLLGRIKNNQEGK KLNLVIKNEEYFEFVQNRNN 4 CasJ MQQYQVSKTVRFGLTLKNSEKKHATHLLLKDLVNVSEERI CasJ (wild type) KNEITKDDKNQSELSFFNEVIETLDLMDKYIKDWENCFYR TDQIQLTKEYYKVIAKKACEDWFWTNDRGMKEPTSSIISF NSLKSSDKSKTSDNLDRKKKILDYWKGNIFKTQKAIKDVL DITEDIQKAIEEKKSHREINRVNHRKMGIHLIHLINDTLV PLCNGSIFEGNISKLDECESENEKLIDEASTEKQDERKEL LSKINEIKQYFEDNGGNVPFARATLNRHTANQKPDRYNEE IKKLVNELGVNSLVRSLKSKTIEEIKTHEEFENKNKINEL KNSFVLSIVEKIQLFKYKTIPASVRFLLADYFEEQKLSTK EEALTIFEEIGKPQNIGFDYIQLKEKDNFTLKKYPLKQAF DYAWENLARLDQNPKANQESVDECKRFEKEVESMEMDNIN EKTYALLLALKEKTTAFDKKGEGAAKNKSEIIEQIKGVFE ELDQPFKIIANTLREEVIKKEDELNVLKRQYRETDRKIKT LQNEIKKIKNQIKNLENSKKYSFPEIIKWIDLTEQEQLLD KNKQAKSNYQKAKGDLGLIRGSQKTSINDYFYLTDKVYRK LAQDFGKKMADLREKLLDKNDVNKIKYLSYIVKDNQGYQY TLLKPLEDKNAEIIELKSEPNGDLKLEEIKSLTSKTLNKF IKNKGAYKEFHSAEFEHKKIKEDWKNYKYNSDFIVKLKKC LSHSDMANTQNWKAFGWDLDKCKSYETIEKEIDQKSYQLV EIKLSKTTIEKWVKENNYLLLPIVNQDITAEKLKVNTNQF TKDWQHIFEKNPNHRLHPEENIAYRQPTKDYAKEGEKRYS REQLTGQEMYEYIPQDANYISRKEQITLFNDKEEQKIQVE TFNNQIAKILNAEDFYVIGIDRGITQLATLCVLNKNGVIQ GGFEIFTREEDYTNKQWKHTKLKENRNILDISNLKVETTV NGEKVLVDLSEVKTYLRDENGEPMKNEKGVILTKDNLQKI KLKQLAYDRKLQYKMQHEPELVLSFLDRLENKEQIPNLLA STKLISAYKEGTAYADIDIEQFWNILQTFQTIVDKEGGIE NAKKTMEERQYTELDASFDLKNGVVANMVGVVKFIMEKYN YKTFIALEDLTFAFGQSIDGINGERLRSTKEDKEVDFKEQ ENSTLAGLGTYHEFEMQLLKKLSKTQIGNEIKHEVPAERS TENYEKIVRKDKNVKAKIVSYPEGIVSFVNPRNTSISCPN CKNANKSNRIKKENDRILCKHNIEKTKGNCGEDTANEDEN KLRAENKGKNFKYISSGDANAAYNIAVKLLEDKIFEINKK 5 GGGTTGTTGTGGGTTGAACCCGTCCCAACCATCATCAACT CGCTAGCCAAACACACGCTTAGGGGCCAAAGCAGTGCTAT AATATGAGTGGTGGCGCTATTATATATAGCGTCAGAGAAC TTAGATCTGATATTCTGATGAAGAAAAAATGACTACTGAC TACGAAAGAAGAAGAAAGGAGCTATAGAGAGAGAAGAGGG GTCGTGTAGTAGTGCTTAAACTGTACATGAACAGCAGTAG TGTTACAGAAGCTAAACTCAACCAGAGCTCCACCAAAGAC AAAGAGGGTCTACTTCCATCACCGTCTTGCTCGGTCACTT GGAGCTCTGTCCATAAATTAAACCCATCGTGGCATATCTG TAGGCATCTACCCCGTCTTCGTCGTCCGTTCCTCACTAGC TACCAAGAGGTCGCCATTATTGCCAACATAGAGTGTACGT GGATGTCTATATATATGCCTACTTGCACCCATATGGC 6 type II CRISPR MKLTPLNYILGLDLGIASVGWAVVEIDEQENPLGLIDVGV WP_014991277.1 RNA-guided RTFDRAEVPKTGESLALARRLARSARRLVKRRADRIKKAK endonuclease RLLKAENILLSADEHLPNDVWQLRVKGLDQKLERQEWAAV Cas9 LLHLLKHRGYLSQRKNESKSENKELGALLSGVETNHQILQ [Actinobacillus SAEYRTPAEIAVKKFHVEDGHIRNQRGAYTHTFSRLDLLA suis] EMELLFQRQTDLGNPHTSAKLLENLTALLMWQKPALAGEA ILKMLGKCTFEPTEYKAAKNSYSAERFVWLTKLNNLRILE QGAERALTDNERFALLDQPYEKAKFTYAQARTMLALPDEA IFKGVRYQGEDKKAVETKTILMEMKAYHQIRKALENADLK AEWNELKNNSELLDDIGTAFSLHKTDEDICRYLDGKLSES ILNALLENLNFDKFIQLSLKALQQILPLMLQGQRYDEAVS AIYGDHYGKKSAEINRLLPTIPADEIRNPVVLRTLTQARK VINAVVRLYGSPARIHIETGREVGKSYQDRKKLEKQQEDN RKQRESAVKKFKEYFPNFVGEPKGKDILKMRLYELQQAKC LYSGKSLELHRLLEKGYVEVDHALPFSRTWDDSFNNKVLV LANENQNKGNLTPYEWLDGKNNSEHWQNEVARVQTSGESH TKKQRILSHKLDEKGFIERNLNDTRYVARFLCNFIADNML LTGKGKRKVFASNGQITALLRGRWGLQKVRDDNDRHHALD AVVVACSTVVMQQKITRFVRYEEGNVFSGERIDRETGEII PLHEPSPWAFFRENVEIRIFSENPKLELENRLPDYPQYNH EFVQPLFVSRMPTRKMTGQGHMETVKSAKRLDEGLSVLKV PLTQLKLSDLERMVNREREVTLYESLKARLEQFGNDPAKA FAEPFHKKGGAVVKAVRVEQTQKSGVLVRDGNGVADNASM VRVDVFTKGGKYFLVPIYTWQVAKGILPNKAVTANVDEID WLEMDESYQFIFTMYPNDLVKVKLKKEEFFGYYGGLDRAT GAIVIKEHDLEKSKGKQGIYRIGVKLALSFEKYQVDELGK NIRPCRPTKRQHVR

The breadth and scope of the present disclosure should not be limited by any of the above-described Examples, but should be defined only in accordance with the preceding embodiments, the following claims, and their equivalents.

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What is claimed is:
 1. A method for increasing Homology Directed Repair (HDR)-mediated genome modification of a plant cell genome, comprising: providing genome editing molecules to a plant cell, wherein the plant cell is exposed to an effective concentration of a composition comprising at least one HDR promoting agent selected from the group consisting of a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; wherein the genome editing molecules comprise an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; whereby the genome editing molecules modify the plant cell genome by HDR at a frequency that is increased in comparison to a control method wherein a control plant cell is provided with the genome editing molecules but is not exposed to at least one of said HDR promoting agents or any combination thereof.
 2. The method of claim 1, wherein the frequency of HDR is increased by at least 1.5-fold, at least 2-fold, or at least 3-fold in comparison to the control.
 3. The method of claim 1, wherein the plant cell is haploid, diploid, or polyploid.
 4. The method of claim 1, wherein the plant cell is in a culture medium, in a plant, or in a plant tissue.
 5. The method of claim 1, wherein the level of at least one oxygen species is lowered in the plant cell by exposure of the plant cell to a hypoxic condition, or by exposure of the plant cell to at least one reactive oxygen species (ROS) concentration lowering agent, or by exposure of the plant cell to both a hypoxic condition and to at least one ROS concentration lowering agent.
 6. The method of claim 5, wherein the hypoxic condition comprises maintaining the cell in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume, or wherein the cell is in a liquid culture medium and the hypoxic condition comprises maintaining the cell and the medium in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume.
 7. The method of claim 5, wherein the reactive oxygen species (ROS) concentration lowering agent comprises an exogenously provided enzymatic ROS scavenging agent, or an exogenously provided non-enzymatic ROS scavenging agent, or a combination thereof.
 8. The method of claim 5, wherein the HDR promoting agent is selected from the group consisting of a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof.
 9. The method of claim 8, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.
 10. The method of claim 1, wherein the HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.
 11. The method of claim 10, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No, 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.
 12. The method of any one of claims 1 to 11, wherein a bioactive analog thereof is: (v) a substitution of a halogen with another halogen; (vi) a substitution of a C1 to C6 alkyl group or a C1 to C6 alkoxy group with a different C1 to C6 alkyl group or a different C1 to C6 alkoxy group, respectively; (vii) a substitution of an unsubstituted phenyl group with a substituted phenyl group, wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen; and/or, (viii) a substitution of a substituted phenyl group with a different substituted phenyl group wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen.
 13. The method of any one of claims 1 to 11, wherein the composition comprising the HDR promoting agent further comprises an agriculturally acceptable adjuvant and/or excipient.
 14. The method of any one of claims 1 to 11, wherein the plant cell is contained or supported by a plant cell culture medium and Ca2+ and/or Mg2+ is provided in the plant cell culture medium at a concentration of about 40 mM to 150 mM.
 15. The method of any one of claims 1 to 11, further comprising the step of isolating and/or growing a plant cell, propagule, or plant obtained from the plant cell comprising the genomic modification, wherein the genome of the plant cell, propagule, or plant comprises the genomic modification.
 16. A system for modification of a plant gene, comprising: (a) a plant cell; (b) at least one HDR promoting agent selected from the group consisting of 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No, 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; and (c) genome editing molecule(s) comprising: an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; (d) wherein the plant cell is associated with, contacts, and/or contains an effective amount of the HDR promoting agent and the genome editing molecule(s).
 17. The system of claim 16, wherein the plant cell is haploid, diploid, or polyploid.
 18. The system of claim 16, wherein the plant cell is in a culture medium, in a plant, or in a plant tissue.
 19. The system of claim 16, wherein the level of at least one oxygen species is lowered in the plant cell by exposure of the plant cell to a hypoxic condition, or by exposure of the plant cell to at least one reactive oxygen species (ROS) concentration lowering agent, or by exposure of the plant cell to both a hypoxic condition and to at least one ROS concentration lowering agent.
 20. The system of claim 19, wherein the hypoxic condition comprises maintaining the cell in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume, or wherein the cell is in a liquid culture medium and the hypoxic condition comprises maintaining the cell and the medium in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume.
 21. The system of claim 19, wherein the reactive oxygen species (ROS) concentration lowering agent comprises an exogenously provided enzymatic ROS scavenging agent, or an exogenously provided non-enzymatic ROS scavenging agent, or a combination thereof.
 22. The system of claim 19, wherein the HDR promoting agent is selected from the group consisting of a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof.
 23. The system of claim 22, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.
 24. The system of claim 16, wherein the HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.
 25. The system of claim 24, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), a bioactive analog thereof, and a plant cell-compatible salt thereof.
 26. The system of any one of claims 16 to 25, wherein a bioactive analog thereof is: (ix) a substitution of a halogen with another halogen; (x) a substitution of a C1 to C6 alkyl group or a C1 to C6 alkoxy group with a different C1 to C6 alkyl group or a different C1 to C6 alkoxy group, respectively; (xi) a substitution of an unsubstituted phenyl group with a substituted phenyl group, wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen; and/or, (xii) a substitution of a substituted phenyl group with a different substituted phenyl group wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen.
 27. The system of any one of claims 16 to 25, wherein the plant cell is contained or supported by a plant cell culture medium and Ca2+ and/or Mg2+ is provided in the plant cell culture medium at a concentration of about 40 mM to 150 mM.
 28. The system of any one of claims 16 to 25, wherein the composition comprising the HDR promoting agent further comprises an agriculturally acceptable adjuvant and/or excipient.
 29. A method for making a plant cell having a genomic modification, comprising: (c) providing genome editing molecules to a plant cell, wherein the plant cell is exposed to an effective amount of at least one HDR promoting agent selected from the group consisting of a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 128-20-1, CAS No. 549505-65-9, CAS No. 1596-84-5, CAS No. 940929-33-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof; wherein the genome editing molecules comprise an RNA-guided nuclease or a polynucleotide encoding an RNA-guided nuclease, a guide RNA or a polynucleotide encoding a guide RNA, and a donor template DNA molecule; (d) whereby the genome editing molecules modify the plant cell genome by homology directed repair (HDR) at a frequency that is increased in comparison to a control; and isolating or propagating a plant cell comprising the genome modification, thereby making the plant cell having a genomic modification.
 30. The method of claim 29, wherein the genome modification comprises homology directed repair (HDR) of the plant cell genome.
 31. The method of claim 29, wherein the frequency of HDR is increased by at least 1.5-fold, 2-fold, or 3-fold in comparison to a control method wherein a control plant cell is provided with the genome editing molecules but is not exposed to the HDR promoting agent.
 32. The method of claim 29, wherein the plant cell is haploid, diploid, or polyploid.
 33. The method of claim 29, wherein the plant cell is in a culture medium, in a plant, or in a plant tissue.
 34. The method of claim 29, wherein the level of at least one oxygen species is lowered in the plant cell by exposure of the plant cell to a hypoxic condition, or by exposure of the plant cell to at least one reactive oxygen species (ROS) concentration lowering agent, or by exposure of the plant cell to both a hypoxic condition and to at least one ROS concentration lowering agent.
 35. The method of claim 34, wherein the hypoxic condition comprises maintaining the cell in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume, or wherein the cell is in a liquid culture medium and the hypoxic condition comprises maintaining the cell and the medium in air comprising an oxygen concentration of about 12% to about 5% oxygen by volume.
 36. The method of claim 34, wherein the reactive oxygen species (ROS) concentration lowering agent comprises an exogenously provided enzymatic ROS scavenging agent, or an exogenously provided non-enzymatic ROS scavenging agent, or a combination thereof.
 37. The method of claim 34, wherein the HDR promoting agent is selected from the group consisting of a 5-substituted 2, 4-thiazolidinedione, CAS No. 102649-78-5, CAS No. 549505-65-9, CAS No. 336113-53-2, CAS No. 146-77-0, CAS No. 28822-58-4, CAS No. 477845-12-8, CAS No. 872573-93-8, CAS No. 724741-75-7, CAS No. 1357171-62-0, CAS No. 715934-43-2, any bioactive analog thereof, a plant cell-compatible salt thereof, an ester thereof, and any combination thereof.
 38. The method of claim 37, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No, 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.
 39. The method of claim 29, wherein the HDR-promoting agent is a 5-substituted 2, 4-thiazolidinedione.
 40. The method of claim 39, wherein the 5-substituted 2, 4-thiazolidinedione is selected from the group consisting of Rosiglitazone (CAS No. 122320-73-4), Edaglitazone (CAS No. 213411-83-7), Ciglitazone (CAS No. 74772-77-3), Lobeglitazone (CAS No. 607723-33-1), Pioglitazone hydrochloride (CAS No. 112529-15-4), Troglitazone (CAS No. 97322-87-7), Mitoglitazone (CAS No. 146062-49-9), Darglitazone (CAS No. 141200-24-0), Englitazone (CAS No. 109229-58-5), Netoglitazone (CAS No. 161600-01-7), Rivoglitazone (CAS No. 185428-18-6), Balaglitazone (CAS No. 199113-98-9), and a plant cell-compatible salt thereof.
 41. The method of any one of claims 29 to 40, wherein a bioactive analog thereof is: (v) a substitution of a halogen with another halogen; (vi) a substitution of a C1 to C6 alkyl group or a C1 to C6 alkoxy group with a different C1 to C6 alkyl group or a different C1 to C6 alkoxy group, respectively; (vii) a substitution of an unsubstituted phenyl group with a substituted phenyl group, wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen; and/or, (viii) a substitution of a substituted phenyl group with a different substituted phenyl group wherein optionally the substitutions in the phenyl group are selected from a methyl, an alkoxy, aminoalkyl, or halogen.
 42. The method of any one of claims 29 to 40, wherein the plant cell in at least step (a) is contained or supported by a plant cell culture medium and Ca²⁺ and/or Mg²⁺ is provided in the plant cell culture medium at a concentration of about 40 mM to 150 mM.
 43. The method of any one of claims 29 to 40, wherein the composition comprising the HDR promoting agent further comprises an agriculturally acceptable adjuvant and/or excipient.
 44. The method of any one of claims 29 to 40, further comprising the step of isolating and/or growing a plant cell, propagule, or plant obtained from the plant cell comprising the genomic modification, wherein the genome of the plant cell, propagule, or plant comprises the genomic modification.
 45. The method of any one of claims 1 to 11 or 29 to 40, wherein the effective concentration of the HDR-promoting agent is about 0.1 μM to about 500 μM.
 46. The method of claim 45, wherein the effective concentration of the HDR-promoting agent is about 0.5 μM to about 50 μM.
 47. The system of any one of claims 16 to 25, wherein the effective concentration of the HDR-promoting agent is about 0.1 μM to about 500 μM.
 48. The system of claim 47, wherein the effective concentration of the HDR-promoting agent is about 0.5 μM to about 50 μM. 